| 1999 | 1 | | 1 | FrRnd | 1 | Devil Rays | Josh Hamilton (minors) | 24.6 | 805 | 3088 | 171 | .296 | .892 | | | | | | | HS | Athens Drive HS (Raleigh, NC) |
| 1999 | 1 | | 5 | FrRnd | 5 | Twins | B.J. Garbe (minors) | | | | | | | | | | | | | HS | Moses Lake HS (Moses Lake, WA) |
| 1999 | 1 | | 17 | FrRnd | 17 | Red Sox via Angels | *Rick Asadoorian (minors) | | | | | | | | | | | | | HS | Northbridge HS (Whitinsville, MA) |
| 1999 | 1 | | 20 | FrRnd | 20 | Padres via Dodgers | *Vince Faison (minors) | | | | | | | | | | | | | HS | Toombs County HS (Lyons, GA) |
| 1999 | 1 | | 21 | FrRnd | 21 | Orioles via Rangers | *Larry Bigbie (minors) | 2.5 | 392 | 1227 | 31 | .267 | .726 | | | | | | | 4Yr | Ball State University (Muncie, IN) |
| 1999 | 1 | | 23 | FrRnd | 23 | Orioles via Indians | *Keith Reed (minors) | -0.1 | 6 | 5 | 0 | .200 | .533 | | | | | | | 4Yr | Providence College (Providence, RI) |
| 1999 | 1s | | 42 | FrRnd | 42 | Astros | *Mike Rosamond (minors) | | | | | | | | | | | | | 4Yr | University of Mississippi (Oxford, MS) |
| 1999 | 2 | | 52 | FrRnd | 1 | Devil Rays | Carl Crawford (minors) | 37.2 | 1447 | 5798 | 123 | .293 | .775 | | | | | | | HS | Jefferson Davis HS (Houston, TX) |
| 1999 | 2 | | 60 | FrRnd | 9 | Athletics | Ryan Ludwick (minors) | 11.8 | 916 | 3063 | 143 | .263 | .800 | | | | | | | 4Yr | University of Nevada-Las Vegas (Las Vegas, NV) |
| 1999 | 2 | | 63 | FrRnd | 12 | Phillies | Jason Cooper (minors) | | | | | | | | | | | | | HS | Moses Lake HS (Moses Lake, WA) |
| 1999 | 2 | | 77 | FrRnd | 26 | Cubs | Mike Mallory (minors) | | | | | | | | | | | | | HS | Dinwiddie HS (Sutherland, VA) |
| 1999 | 2 | | 78 | FrRnd | 27 | Yankees | Tommy Winrow (minors) | | | | | | | | | | | | | HS | Bishop Verot HS (Fort Myers, FL) |
| 1999 | 3 | | 92 | FrRnd | 8 | Pirates | Aron Weston (minors) | | | | | | | | | | | | | HS | Solon HS (Solon, IA) |
| 1999 | 3 | | 107 | FrRnd | 23 | Indians | Eric Johnson (minors) | | | | | | | | | | | | | 4Yr | Western Carolina University (Cullowhee, NC) |
| 1999 | 3 | | 109 | FrRnd | 25 | Red Sox | Antron Seiber (minors) | | | | | | | | | | | | | HS | Independence HS (Tickfaw, LA) |
| 1999 | 4 | | 117 | FrRnd | 3 | Tigers | Cody Ross (minors) | 12.1 | 941 | 3098 | 124 | .261 | .775 | 1 | 0 | 0 | 0.00 | 1.00 | 0 | HS | Carlsbad HS (Carlsbad, NM) |
| 1999 | 4 | | 118 | FrRnd | 4 | Rangers via Diamondbacks | *Kevin Mench (minors) | 5.5 | 729 | 2362 | 89 | .268 | .780 | | | | | | | 4Yr | University of Delaware (Newark, DE) |
| 1999 | 4 | | 120 | FrRnd | 6 | Expos | Matthew Cepicky (minors) | -0.9 | 89 | 185 | 4 | .211 | .575 | | | | | | | 4Yr | Missouri State University (Springfield, MO) |
| 1999 | 4 | | 127 | FrRnd | 13 | Cardinals via Orioles | *Ben Johnson (minors) | 0.3 | 98 | 222 | 7 | .230 | .728 | | | | | | | HS | Germantown HS (Germantown, TN) |
| 1999 | 4 | | 136 | FrRnd | 22 | Mets | Angel Pagan (minors) | 15.6 | 741 | 2601 | 44 | .280 | .752 | | | | | | | HS | Republica De Colombia HS (Rio Piedras, PR) |
| 1999 | 4 | | 143 | FrRnd | 29 | Astros | Jon Topolski (minors) | | | | | | | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 1999 | 4 | | 144 | FrRnd | 30 | Braves | Alec Zumwalt (minors) | | | | | | | | | | | | | HS | East Forsyth Sr. HS (Kernersville, NC) |
| 1999 | 5 | | 147 | FrRnd | 3 | Tigers | Dayle Campbell (minors) | | | | | | | | | | | | | JC | Los Angeles Pierce College (Woodland Hills, CA) |
| 1999 | 5 | | 160 | FrRnd | 16 | Rockies | Chris Testa (minors) | | | | | | | | | | | | | HS | Palmdale HS (Palmdale, CA) |
| 1999 | 5 | | 162 | FrRnd | 18 | Cardinals | Charlie Williams (minors) | | | | | | | | | | | | | 4Yr | Rice University (Houston, TX) |
| 1999 | 6 | | 176 | FrRnd | 2 | Marlins | Charlie Frazier (minors) | | | | | | | | | | | | | HS | Toms River South HS (Toms River, NJ) |
| 1999 | 6 | | 180 | FrRnd | 6 | Expos | Dominick Ambrosini (minors) | | | | | | | | | | | | | HS | Connetquot HS (Ronkonkoma, NY) |
| 1999 | 6 | | 182 | FrRnd | 8 | Pirates | B.J. Barns (minors) | | | | | | | | | | | | | 4Yr | Duquesne University (Pittsburgh, PA) |
| 1999 | 6 | | 188 | FrRnd | 14 | Reds | Alex LeFlore (minors) | | | | | | | | | | | | | HS | Pinellas Park HS (Pinellas Park, FL) |
| 1999 | 6 | | 194 | FrRnd | 20 | Dodgers | Shane Victorino (minors) | 26.0 | 1118 | 4007 | 92 | .275 | .767 | | | | | | | HS | St. Anthony HS (Wailuku, HI) |
| 1999 | 6 | | 198 | FrRnd | 24 | Giants | Ryan Pene (minors) | | | | | | | | | | | | | 4Yr | Dixie State College of Utah (St. George, UT) |
| 1999 | 6 | | 199 | FrRnd | 25 | Red Sox | Jon Kail (minors) | | | | | | | | | | | | | HS | Baldwin HS (Pittsburgh, PA) |
| 1999 | 6 | | 203 | FrRnd | 29 | Astros | Jason Lane (minors) | 1.4 | 497 | 1208 | 61 | .241 | .771 | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 1999 | 7 | | 209 | FrRnd | 5 | Twins | Darren Ciraco (minors) | | | | | | | | | | | | | HS | Pelham Memorial HS (Pelham, NY) |
| 1999 | 7 | | 212 | FrRnd | 8 | Pirates | Matt Schneider (minors) | | | | | | | | | | | | | 4Yr | University of North Florida (Jacksonville, FL) |
| 1999 | 7 | | 218 | FrRnd | 14 | Reds | Corey Barrow (minors) | | | | | | | | | | | | | HS | Clarke Central HS (Athens, GA) |
| 1999 | 7 | | 224 | FrRnd | 20 | Dodgers | Jose Escalera (minors) | | | | | | | | | | | | | HS | Carlos Escobar Lopez HS (Loiza, PR) |
| 1999 | 7 | | 227 | FrRnd | 23 | Indians | Daylon Monette (minors) | | | | | | | | | | | | | HS | A. B. Miller HS (Fontana, CA) |
| 1999 | 8 | | 245 | FrRnd | 11 | Mariners | Terrmel Sledge (minors) | 0.4 | 291 | 705 | 25 | .247 | .745 | | | | | | | 4Yr | California State University Long Beach (Long Beach, CA) |
| 1999 | 8 | | 250 | FrRnd | 16 | Rockies | Greg Catalanotte (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 1999 | 8 | | 256 | FrRnd | 22 | Mets | Forrest Lawson (minors) | | | | | | | | | | | | | HS | John R Rogers HS (Puyallup, WA) |
| 1999 | 8 | | 262 | FrRnd | 28 | Padres | Todd Donovan (minors) | | | | | | | | | | | | | 4Yr | Siena College (Loudonville, NY) |
| 1999 | 9 | | 273 | FrRnd | 9 | Athletics | Kirk Asche (minors) | | | | | | | | | | | | | 4Yr | Jacksonville University (Jacksonville, FL) |
| 1999 | 9 | | 285 | FrRnd | 21 | Rangers | Brett Cadiente (minors) | | | | | | | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 1999 | 9 | | 286 | FrRnd | 22 | Mets | Wayne Lydon (minors) | | | | | | | | | | | | | HS | Valley View HS (Archbald, PA) |
| 1999 | 9 | | 294 | FrRnd | 30 | Braves | Angelo Burrows (minors) | | | | | | | | | | | | | HS | Killian HS (Miami, FL) |
| 1999 | 10 | | 296 | FrRnd | 2 | Marlins | Scott Goodman (minors) | | | | | | | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 1999 | 10 | | 306 | FrRnd | 12 | Phillies | Marlon Byrd (minors) | 17.2 | 1156 | 4005 | 93 | .277 | .751 | | | | | | | JC | Georgia Perimeter College (Covington, GA) |
| 1999 | 10 | | 314 | FrRnd | 20 | Dodgers | Lamont Matthews (minors) | | | | | | | | | | | | | 4Yr | Oklahoma State University (Stillwater, OK) |
| 1999 | 10 | | 315 | FrRnd | 21 | Rangers | Jason Bryan (minors) | | | | | | | | | | | | | HS | New Utrecht HS (Brooklyn, NY) |
| 1999 | 10 | | 316 | FrRnd | 22 | Mets | Prentice Redman (minors) | -0.4 | 15 | 24 | 1 | .125 | .484 | | | | | | | JC | Bevill State Community College (Sumiton, AL) |
| 1999 | 10 | | 319 | FrRnd | 25 | Red Sox | Brian Wiese (minors) | | | | | | | | | | | | | 4Yr | Mississippi State University (Mississippi State, MS) |
| 1999 | 10 | | 321 | FrRnd | 27 | Yankees | Brad Ticehurst (minors) | | | | | | | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 1999 | 11 | | 330 | FrRnd | 6 | Expos | David Lutz (minors) | | | | | | | | | | | | | HS | Monte Vista HS (Spring Valley, CA) |
| 1999 | 11 | | 333 | FrRnd | 9 | Athletics | Michael Wenner (minors) | | | | | | | | | | | | | 4Yr | Rider University (Lawrenceville, NJ) |
| 1999 | 11 | | 334 | FrRnd | 10 | Brewers | Will Ford (minors) | | | | | | | | | | | | | 4Yr | Rice University (Houston, TX) |
| 1999 | 12 | | 357 | FrRnd | 3 | Tigers | Daniel Davis (minors) | | | | | | | | | | | | | HS | Osceola HS (Kissimmee, FL) |
| 1999 | 12 | | 358 | FrRnd | 4 | Diamondbacks | Doug DeVore (minors) | 0.1 | 50 | 107 | 3 | .224 | .646 | | | | | | | 4Yr | Indiana University-Bloomington (Bloomington, IN) |
| 1999 | 12 | | 360 | FrRnd | 6 | Expos | Brian Stavisky (minors) | | | | | | | | | | | | | HS | Port Allegany HS (Port Allegany, PA) |
| 1999 | 12 | | 363 | FrRnd | 9 | Athletics | Jay Garthwaite (minors) | | | | | | | | | | | | | HS | Meridian HS (Kent, WA) |
| 1999 | 12 | | 365 | FrRnd | 11 | Mariners | Larry Brown (minors) | | | | | | | | | | | | | HS | San Fernando HS (San Fernando, CA) |
| 1999 | 12 | | 366 | FrRnd | 12 | Phillies | Brian Bush (minors) | | | | | | | | | | | | | 4Yr | University of Michigan (Ann Arbor, MI) |
| 1999 | 12 | | 369 | FrRnd | 15 | White Sox | Derek Stanley (minors) | | | | | | | | | | | | | JC | North Florida Community College (Madison, FL) |
| 1999 | 12 | | 371 | FrRnd | 17 | Angels | Mike O'Keefe (minors) | | | | | | | | | | | | | 4Yr | Providence College (Providence, RI) |
| 1999 | 12 | | 379 | FrRnd | 25 | Red Sox | Lew Ford (minors) | 8.3 | 519 | 1585 | 35 | .268 | .744 | | | | | | | 4Yr | Dallas Baptist University (Dallas, TX) |
| 1999 | 12 | | 380 | FrRnd | 26 | Cubs | Condor Cash (minors) | | | | | | | | | | | | | HS | Stephens County School (Toccoa, GA) |
| 1999 | 13 | | 394 | FrRnd | 10 | Brewers | Terry Mayo (minors) | | | | | | | | | | | | | HS | Eastern Guilford HS (Greensboro, NC) |
| 1999 | 13 | | 399 | FrRnd | 15 | White Sox | Casey Rogowski (minors) | | | | | | | | | | | | | HS | Catholic Central HS (Redford, MI) |
| 1999 | 13 | | 405 | FrRnd | 21 | Rangers | Jason Jones (minors) | -0.2 | 40 | 107 | 3 | .215 | .653 | | | | | | | 4Yr | Kennesaw State University (Kennesaw, GA) |
| 1999 | 14 | | 421 | FrRnd | 7 | Royals | Jarrett Shearin (minors) | | | | | | | | | | | | | 4Yr | University of North Carolina at Chapel Hill (Chapel Hill, NC) |
| 1999 | 14 | | 422 | FrRnd | 8 | Pirates | Daniel Hudson (minors) | | | | | | | | | | | | | JC | Mississippi Gulf Coast Community College (Perkinston, MS) |
| 1999 | 14 | | 424 | FrRnd | 10 | Brewers | Steve Truitt (minors) | | | | | | | | | | | | | 4Yr | Texas A&M University (College Station, TX) |
| 1999 | 14 | | 426 | FrRnd | 12 | Phillies | Jovanathan Clark (minors) | | | | | | | | | | | | | HS | Vallejo HS (Vallejo, CA) |
| 1999 | 14 | | 427 | FrRnd | 13 | Orioles | Matt Riordan (minors) | | | | | | | | | | | | | 4Yr | Loyola Marymount University (Los Angeles, CA) |
| 1999 | 14 | | 429 | FrRnd | 15 | White Sox | Spencer Oborn (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 1999 | 14 | | 435 | FrRnd | 21 | Rangers | Ernest Villegas (minors) | | | | | | | | | | | | | JC | Northeast Texas Community College (Mount Pleasant, TX) |
| 1999 | 15 | | 446 | FrRnd | 2 | Marlins | Barry Schell (minors) | | | | | | | | | | | | | JC | Palomar College (San Marcos, CA) |
| 1999 | 15 | | 447 | FrRnd | 3 | Tigers | Corey Richardson (minors) | | | | | | | | | | | | | 4Yr | New Mexico State University (Las Cruces, NM) |
| 1999 | 15 | | 457 | FrRnd | 13 | Orioles | James Ralph (minors) | | | | | | | | | | | | | 4Yr | University of Wyoming (Laramie, WY) |
| 1999 | 16 | | 479 | FrRnd | 5 | Twins | Kevin West (minors) | | | | | | | | | | | | | JC | Mendocino College (Ukiah, CA) |
| 1999 | 16 | | 483 | FrRnd | 9 | Athletics | Matt Allegra (minors) | | | | | | | | | | | | | HS | Lake Mary HS (Lake Mary, FL) |
| 1999 | 16 | | 484 | FrRnd | 10 | Brewers | Jason Tibesar (minors) | | | | | | | | | | | | | JC | South Mountain Community College (Phoenix, AZ) |
| 1999 | 16 | | 485 | FrRnd | 11 | Mariners | Sean Parnell (minors) | | | | | | | | | | | | | 4Yr | University of Wisconsin at Madison (Madison, WI) |
| 1999 | 16 | | 489 | FrRnd | 15 | White Sox | Ben Birk (minors) | | | | | | | | | | | | | 4Yr | University of Minnesota (Minneapolis, MN) |
| 1999 | 16 | | 491 | FrRnd | 17 | Angels | Brandon Jackson (minors) | | | | | | | | | | | | | 4Yr | Savannah State University (Savannah, GA) |
| 1999 | 16 | | 498 | FrRnd | 24 | Giants | Micah Holst (minors) | | | | | | | | | | | | | 4Yr | Missouri State University (Springfield, MO) |
| 1999 | 16 | | 502 | FrRnd | 28 | Padres | Greg Ienni (minors) | | | | | | | | | | | | | 4Yr | California State University Los Angeles (Los Angeles, CA) |
| 1999 | 17 | | 505 | FrRnd | 1 | Devil Rays | Matt Diaz (minors) | 3.6 | 736 | 1881 | 45 | .290 | .767 | | | | | | | 4Yr | Florida State University (Tallahassee, FL) |
| 1999 | 17 | | 521 | FrRnd | 17 | Angels | Scott Bikowski (minors) | | | | | | | | | | | | | 4Yr | Florida Southern College (Lakeland, FL) |
| 1999 | 17 | | 523 | FrRnd | 19 | Blue Jays | Reed Johnson (minors) | 11.6 | 1156 | 3361 | 63 | .283 | .751 | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 1999 | 17 | | 525 | FrRnd | 21 | Rangers | Orlando Cruz (minors) | | | | | | | | | | | | | HS | Jose Collazo Colon HS (Juncos, PR) |
| 1999 | 17 | | 530 | FrRnd | 26 | Cubs | Derrick Cohens (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 1999 | 18 | | 543 | FrRnd | 9 | Athletics | G.W. Keller (minors) | | | | | | | | | | | | | 4Yr | University of Alabama (Tuscaloosa, AL) |
| 1999 | 18 | | 545 | FrRnd | 11 | Mariners | Kris Gundrum (minors) | | | | | | | | | | | | | 4Yr | Western Michigan University (Kalamazoo, MI) |
| 1999 | 18 | | 563 | FrRnd | 29 | Astros | Mike Hill (minors) | | | | | | | | | | | | | 4Yr | Oral Roberts University (Tulsa, OK) |
| 1999 | 19 | | 567 | FrRnd | 3 | Tigers | Casey Williamson (minors) | | | | | | | | | | | | | 4Yr | Troy University (Troy, AL) |
| 1999 | 19 | | 570 | FrRnd | 6 | Expos | Pierre Blount (minors) | | | | | | | | | | | | | HS | Colton HS (Colton, CA) |
| 1999 | 19 | | 571 | FrRnd | 7 | Royals | Jermaine Smiley (minors) | | | | | | | | | | | | | JC | Bellevue Community College (Bellevue, WA) |
| 1999 | 19 | | 581 | FrRnd | 17 | Angels | Gary Johnson (minors) | 0.1 | 5 | 8 | 0 | .375 | .944 | | | | | | | 4Yr | Brigham Young University (Provo, UT) |
| 1999 | 19 | | 582 | FrRnd | 18 | Cardinals | Christopher Beck (minors) | | | | | | | | | | | | | 4Yr | California State University Fullerton (Fullerton, CA) |
| 1999 | 19 | | 587 | FrRnd | 23 | Indians | Travis Santini (minors) | | | | | | | | | | | | | HS | Lely HS (Naples, FL) |
| 1999 | 20 | | 598 | FrRnd | 4 | Diamondbacks | Justin Graham (minors) | | | | | | | | | | | | | 4Yr | West Virginia State University (Institute, WV) |
| 1999 | 20 | | 607 | FrRnd | 13 | Orioles | Steve Salargo (minors) | | | | | | | | | | | | | 4Yr | East Carolina University (Greenville, NC) |
| 1999 | 20 | | 615 | FrRnd | 21 | Rangers | Kevin Marshall (minors) | | | | | | | | | | | | | HS | James W. Martin HS (Arlington, TX) |
| 1999 | 20 | | 624 | FrRnd | 30 | Braves | Collin Remekie (minors) | | | | | | | | | | | | | HS | Martin County HS (Stuart, FL) |
| 1999 | 21 | | 636 | FrRnd | 12 | Phillies | Aaron Merhoff (minors) | | | | | | | | | | | | | 4Yr | Texas Lutheran University (Seguin, TX) |
| 1999 | 21 | | 644 | FrRnd | 20 | Dodgers | Chris Snow (minors) | | | | | | | | | | | | | HS | Desert Vista HS (Phoenix, AZ) |
| 1999 | 21 | | 645 | FrRnd | 21 | Rangers | Mike Falco (minors) | | | | | | | | | | | | | HS | Agoura HS (Agoura Hills, CA) |
| 1999 | 21 | | 646 | FrRnd | 22 | Mets | Adam Manley (minors) | | | | | | | | | | | | | JC | College of Southern Idaho (Twin Falls, ID) |
| 1999 | 22 | | 656 | FrRnd | 2 | Marlins | James Close (minors) | | | | | | | | | | | | | 4Yr | University of Nevada-Las Vegas (Las Vegas, NV) |
| 1999 | 22 | | 659 | FrRnd | 5 | Twins | Ricky Manning (minors) | | | | | | | | | | | | | HS | Edison HS (Fresno, CA) |
| 1999 | 22 | | 662 | FrRnd | 8 | Pirates | Jason Wilson (minors) | | | | | | | | | | | | | HS | San Augustine HS (San Augustine, TX) |
| 1999 | 22 | | 663 | FrRnd | 9 | Athletics | Edmund Muth (minors) | | | | | | | | | | | | | 4Yr | Stanford University (Palo Alto, CA) |
| 1999 | 22 | | 670 | FrRnd | 16 | Rockies | Darin Naatjes (minors) | | | | | | | | | | | | | HS | West Lyon Jr Sr HS (Alvord, IA) |
| 1999 | 22 | | 672 | FrRnd | 18 | Cardinals | Mike Floyd (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 1999 | 22 | | 676 | FrRnd | 22 | Mets | Kyle Woods (minors) | | | | | | | | | | | | | 4Yr | University of Washington (Seattle, WA) |
| 1999 | 22 | | 678 | FrRnd | 24 | Giants | Jason Barrow (minors) | | | | | | | | | | | | | JC | Chemeketa Community College (Salem, OR) |
| 1999 | 23 | | 692 | FrRnd | 8 | Pirates | Mike Piercy (minors) | | | | | | | | | | | | | 4Yr | Kean University (Union, NJ) |
| 1999 | 23 | | 693 | FrRnd | 9 | Athletics | Mike Lockwood (minors) | | | | | | | | | | | | | 4Yr | The Ohio State University (Columbus, OH) |
| 1999 | 23 | | 703 | FrRnd | 19 | Blue Jays | Andre Monroe (minors) | | | | | | | | | | | | | HS | Santa Monica HS (Santa Monica, CA) |
| 1999 | 23 | | 704 | FrRnd | 20 | Dodgers | Reggie Abercrombie (minors) | -0.2 | 180 | 386 | 9 | .223 | .629 | | | | | | | HS | Columbus HS (Columbus, GA) |
| 1999 | 23 | | 705 | FrRnd | 21 | Rangers | Charles Summerall (minors) | | | | | | | | | | | | | HS | Armwood HS (Armwood, FL) |
| 1999 | 24 | | 724 | FrRnd | 10 | Brewers | Ryan Knox (minors) | | | | | | | | | | | | | 4Yr | Illinois State University (Normal, IL) |
| 1999 | 24 | | 726 | FrRnd | 12 | Phillies | Joe Schley (minors) | | | | | | | | | | | | | 4Yr | Southern Illinois University Carbondale (Carbondale, IL) |
| 1999 | 24 | | 729 | FrRnd | 15 | White Sox | Todd Holt (minors) | | | | | | | | | | | | | JC | Louisburg College (Louisburg, NC) |
| 1999 | 24 | | 740 | FrRnd | 26 | Cubs | Kevin Collins (minors) | | | | | | | | | | | | | HS | Land O'Lakes HS (Land O'Lakes, FL) |
| 1999 | 25 | | 772 | FrRnd | 28 | Padres | Tony Vandemore (minors) | | | | | | | | | | | | | 4Yr | Truman State University (Kirksville, MO) |
| 1999 | 26 | | 778 | FrRnd | 4 | Diamondbacks | Kevan Burns (minors) | | | | | | | | | | | | | 4Yr | Troy University (Troy, AL) |
| 1999 | 26 | | 796 | FrRnd | 22 | Mets | Brad Wright (minors) | | | | | | | | | | | | | 4Yr | University of California, Santa Barbara (Santa Barbara, CA) |
| 1999 | 26 | | 800 | FrRnd | 26 | Cubs | Ben Johnstone (minors) | | | | | | | | | | | | | 4Yr | Yale University (New Haven, CT) |
| 1999 | 27 | | 807 | FrRnd | 3 | Tigers | Johnny Gordon (minors) | | | | | | | | | | | | | 4Yr | Warner Southern College (Lake Wales, FL) |
| 1999 | 27 | | 815 | FrRnd | 11 | Mariners | Andrew Rempel (minors) | | | | | | | | | | | | | HS | W.J. Mount HS (Abbottsford, BC) |
| 1999 | 27 | | 819 | FrRnd | 15 | White Sox | Daniel Ortmeier (minors) | -0.7 | 124 | 255 | 6 | .255 | .721 | | | | | | | HS | Lewisville HS (Lewisville, TX) |
| 1999 | 27 | | 823 | FrRnd | 19 | Blue Jays | Angel Molina (minors) | | | | | | | | | | | | | HS | Colegio Cristo Rey HS (Santa Isabel, PR) |
| 1999 | 27 | | 828 | FrRnd | 24 | Giants | Troy Gustafson (minors) | | | | | | | | | | | | | HS | Blaine HS (Blaine, MN) |
| 1999 | 27 | | 832 | FrRnd | 28 | Padres | Christopher Adolph (minors) | | | | | | | | | | | | | 4Yr | University of Nevada-Reno (Reno, NV) |
| 1999 | 28 | | 860 | FrRnd | 26 | Cubs | David Lemon (minors) | | | | | | | | | | | | | HS | Eustis HS (Eustis, FL) |
| 1999 | 29 | | 873 | FrRnd | 9 | Athletics | Andre Marshall (minors) | | | | | | | | | | | | | JC | Walla Walla Community College (Walla Walla, WA) |
| 1999 | 29 | | 880 | FrRnd | 16 | Rockies | Bryce Coppieters (minors) | | | | | | | | | | | | | JC | Lethbridge CC (Lethbridge, AB) |
| 1999 | 29 | | 882 | FrRnd | 18 | Cardinals | Justin Albertson (minors) | | | | | | | | | | | | | JC | El Camino College (Torrance, CA) |
| 1999 | 29 | | 888 | FrRnd | 24 | Giants | Troy Ransom (minors) | | | | | | | | | | | | | JC | South Mountain Community College (Phoenix, AZ) |
| 1999 | 29 | | 892 | FrRnd | 28 | Padres | Barry Long (minors) | | | | | | | | | | | | | HS | Evans HS (Martinez, GA) |
| 1999 | 30 | | 897 | FrRnd | 3 | Tigers | Joseph Urban (minors) | | | | | | | | | | | | | JC | Santa Ana College (Santa Ana, CA) |
| 1999 | 30 | | 903 | FrRnd | 9 | Athletics | Dwight Edge (minors) | | | | | | | | | | | | | 4Yr | University of Tampa (Tampa, FL) |
| 1999 | 30 | | 904 | FrRnd | 10 | Brewers | Robert Pregnolato (minors) | | | | | | | | | | | | | HS | Palm Beach Atlantic HS (Burlington, ON) |
| 1999 | 30 | | 907 | FrRnd | 13 | Orioles | Kyle Yudizky (minors) | | | | | | | | | | | | | HS | Duncanville HS (Duncanville, TX) |
| 1999 | 30 | | 908 | FrRnd | 14 | Reds | Jon Sheaffer (minors) | | | | | | | | | | | | | JC | South Mountain Community College (Phoenix, AZ) |
| 1999 | 30 | | 909 | FrRnd | 15 | White Sox | Jon Cavin (minors) | | | | | | | | | | | | | JC | Connors State College (Warner, OK) |
| 1999 | 30 | | 918 | FrRnd | 24 | Giants | Ryan Davis (minors) | | | | | | | | | | | | | JC | Cosumnes River College (Sacramento, CA) |
| 1999 | 30 | | 920 | FrRnd | 26 | Cubs | Ray Sadler (minors) | -0.1 | 3 | 8 | 1 | .250 | .875 | | | | | | | JC | Hill College (Hillsboro, TX) |
| 1999 | 30 | | 922 | FrRnd | 28 | Padres | Jason Hammond (minors) | | | | | | | | | | | | | HS | West Hills HS (Santee, CA) |
| 1999 | 31 | | 931 | FrRnd | 7 | Royals | Jason Crear (minors) | | | | | | | | | | | | | HS | CE King HS (Houston, TX) |
| 1999 | 31 | | 933 | FrRnd | 9 | Athletics | Kris Mancini (minors) | | | | | | | | | | | | | JC | Community College of Rhode Island (Warwick, RI) |
| 1999 | 31 | | 936 | FrRnd | 12 | Phillies | Wade Van Vark (minors) | | | | | | | | | | | | | 4Yr | Central College (Pella, IA) |
| 1999 | 31 | | 938 | FrRnd | 14 | Reds | Corey Ward (minors) | | | | | | | | | | | | | JC | Odessa College (Odessa, TX) |
| 1999 | 31 | | 939 | FrRnd | 15 | White Sox | Juan Gutierrez (minors) | | | | | | | | | | | | | HS | Coral Park HS (Miami, FL) |
| 1999 | 31 | | 944 | FrRnd | 20 | Dodgers | Justin Glenn (minors) | | | | | | | | | | | | | HS | Sheridan HS (Little Rock, AR) |
| 1999 | 31 | | 948 | FrRnd | 24 | Giants | Scott Daeley (minors) | | | | | | | | | | | | | 4Yr | Wake Forest University (Winston-Salem, NC) |
| 1999 | 31 | | 949 | FrRnd | 25 | Red Sox | Jaime Bubela (minors) | -0.1 | 11 | 19 | 0 | .105 | .255 | | | | | | | 4Yr | Baylor University (Waco, TX) |
| 1999 | 31 | | 952 | FrRnd | 28 | Padres | Jarett Roenicke (minors) | | | | | | | | | | | | | JC | Yuba CC (Marysvale, CA) |
| 1999 | 32 | | 966 | FrRnd | 12 | Phillies | Jay Sitzman (minors) | | | | | | | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 1999 | 32 | | 967 | FrRnd | 13 | Orioles | Kevin Virtue (minors) | | | | | | | | | | | | | HS | A B Lucas Secondary School (London, ON) |
| 1999 | 32 | | 969 | FrRnd | 15 | White Sox | Michel Valdez (minors) | | | | | | | | | | | | | JC | Miami-Dade College (Miami, FL) |
| 1999 | 32 | | 971 | FrRnd | 17 | Angels | Chris Hills (minors) | | | | | | | | | | | | | 4Yr | Jackson State University (Jackson, MS) |
| 1999 | 32 | | 973 | FrRnd | 19 | Blue Jays | Aaron Fera (minors) | | | | | | | | | | | | | 4Yr | Georgia College and State University (Milledgeville, GA) |
| 1999 | 32 | | 977 | FrRnd | 23 | Indians | Benjamin Fransico (minors) | | | | | | | | | | | | | HS | Servite HS (Anaheim, CA) |
| 1999 | 32 | | 979 | FrRnd | 25 | Red Sox | David Flournoy (minors) | | | | | | | | | | | | | HS | Deer Valley HS (Antioch, CA) |
| 1999 | 32 | | 980 | FrRnd | 26 | Cubs | Jorge Acevedo (minors) | | | | | | | | | | | | | HS | Efrain Sanchez Hidalgo HS (Moca, PR) |
| 1999 | 32 | | 984 | FrRnd | 30 | Braves | Joseph Francisco (minors) | | | | | | | | | | | | | 4Yr | Wagner College (Staten Island, NY) |
| 1999 | 33 | | 989 | FrRnd | 5 | Twins | Billy Keppinger (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 1999 | 33 | | 990 | FrRnd | 6 | Expos | Victor Rosario (minors) | | | | | | | | | | | | | HS | Sandalwood HS (Jacksonville, FL) |
| 1999 | 33 | | 993 | FrRnd | 9 | Athletics | Alex Coleman (minors) | | | | | | | | | | | | | HS | Polytechnic HS (Long Beach, CA) |
| 1999 | 33 | | 995 | FrRnd | 11 | Mariners | Chuck Lopez (minors) | | | | | | | | | | | | | 4Yr | California State University Long Beach (Long Beach, CA) |
| 1999 | 33 | | 1009 | FrRnd | 25 | Red Sox | Perry Miley (minors) | | | | | | | | | | | | | 4Yr | William Carey College (Hattiesburg, MS) |
| 1999 | 33 | | 1010 | FrRnd | 26 | Cubs | Greg Hanoian (minors) | | | | | | | | | | | | | 4Yr | University of Southern California (Los Angeles, CA) |
| 1999 | 33 | | 1013 | FrRnd | 29 | Astros | Steve Hoover (minors) | | | | | | | | | | | | | 4Yr | California State University Stanislaus (Turlock, CA) |
| 1999 | 34 | | 1019 | FrRnd | 5 | Twins | John Thomman (minors) | | | | | | | | | | | | | HS | Levelland HS (Levelland, TX) |
| 1999 | 34 | | 1023 | FrRnd | 9 | Athletics | Geoff Comfort (minors) | | | | | | | | | | | | | JC | College of San Mateo (San Mateo, CA) |
| 1999 | 34 | | 1034 | FrRnd | 20 | Dodgers | Nom Siriveaw (minors) | | | | | | | | | | | | | JC | East Oklahoma State College (Wilburton, OK) |
| 1999 | 34 | | 1036 | FrRnd | 22 | Mets | Pat O'Sullivan (minors) | | | | | | | | | | | | | 4Yr | Austin Peay State University (Clarksville, TN) |
| 1999 | 34 | | 1037 | FrRnd | 23 | Indians | Kerry Hodges (minors) | | | | | | | | | | | | | JC | New Mexico Junior College (Hobbs, NM) |
| 1999 | 35 | | 1046 | FrRnd | 2 | Marlins | Enrique Mendieta (minors) | | | | | | | | | | | | | 4Yr | Norfolk State University (Norfolk, VA) |
| 1999 | 35 | | 1051 | FrRnd | 7 | Royals | Marcus Wyatt (minors) | | | | | | | | | | | | | HS | Fontana HS (Fontana, CA) |
| 1999 | 35 | | 1069 | FrRnd | 25 | Red Sox | Ben Marbury (minors) | | | | | | | | | | | | | | |
| 1999 | 35 | | 1070 | FrRnd | 26 | Cubs | Eduardo Marquez (minors) | | | | | | | | | | | | | 4Yr | Nicholls State University (Thibodaux, LA) |
| 1999 | 36 | | 1075 | FrRnd | 1 | Devil Rays | Ralph Roberts (minors) | | | | | | | | | | | | | 4Yr | Lenoir-Rhyne College (Hickory, NC) |
| 1999 | 36 | | 1076 | FrRnd | 2 | Marlins | Kevin Snowden (minors) | | | | | | | | | | | | | HS | Eleanor Roosevelt HS (Lanham, MD) |
| 1999 | 36 | | 1081 | FrRnd | 7 | Royals | Julian Gonzalez (minors) | | | | | | | | | | | | | 4Yr | University of Virginia (Charlottesville, VA) |
| 1999 | 36 | | 1097 | FrRnd | 23 | Indians | Jerad Doty (minors) | | | | | | | | | | | | | HS | Rio Vista HS (Rio Vista, TX) |
| 1999 | 36 | | 1098 | FrRnd | 24 | Giants | Bryan Lang (minors) | | | | | | | | | | | | | JC | Scottsdale Community College (Scottsdale, AZ) |
| 1999 | 36 | | 1099 | FrRnd | 25 | Red Sox | John Brandon (minors) | | | | | | | | | | | | | JC | Panola College (Carthage, TX) |
| 1999 | 36 | | 1102 | FrRnd | 28 | Padres | Anthony Bianucci (minors) | | | | | | | | | | | | | HS | Woodson HS (Annandale, VA) |
| 1999 | 37 | | 1109 | FrRnd | 5 | Twins | Digno Torres (minors) | | | | | | | | | | | | | JC | Florida Gateway College (Lake City, FL) |
| 1999 | 37 | | 1118 | FrRnd | 14 | Reds | Jerymane Beasley (minors) | | | | | | | | | | | | | 4Yr | Eastern Washington University (Cheney, WA) |
| 1999 | 37 | | 1119 | FrRnd | 15 | White Sox | Kade Eady (minors) | | | | | | | | | | | | | HS | West Ouacita HS (West Monroe, LA) |
| 1999 | 37 | | 1120 | FrRnd | 16 | Rockies | Chad Liter (minors) | | | | | | | | | | | | | HS | Madison Consolidated HS (Madison, IN) |
| 1999 | 38 | | 1136 | FrRnd | 2 | Marlins | Robert Glaser (minors) | | | | | | | | | | | | | JC | San Joaquin Delta College (Stockton, CA) |
| 1999 | 38 | | 1147 | FrRnd | 13 | Orioles | Charlie Dees (minors) | | | | | | | | | | | | | JC | Chipola College (Marianna, FL) |
| 1999 | 38 | | 1152 | FrRnd | 18 | Cardinals | Chris Buckley (minors) | | | | | | | | | | | | | JC | North Arkansas College (Bentonville, AR) |
| 1999 | 38 | | 1161 | FrRnd | 27 | Yankees | Mike Brown (minors) | | | | | | | | | | | | | HS | Centreville HS (Dayton, OH) |
| 1999 | 38 | | 1162 | FrRnd | 28 | Padres | Marcellus Dawson (minors) | | | | | | | | | | | | | HS | Wauwatosa East HS (Wauwatosa, WI) |
| 1999 | 38 | | 1163 | FrRnd | 29 | Astros | Deshain Beasley (minors) | | | | | | | | | | | | | HS | Kamiakin HS (Kennewick, WA) |
| 1999 | 39 | | 1170 | FrRnd | 6 | Expos | Travis Edwards (minors) | | | | | | | | | | | | | JC | Cerritos College (Norwalk, CA) |
| 1999 | 39 | | 1180 | FrRnd | 16 | Rockies | Billy Dennis (minors) | | | | | | | | | | | | | HS | Devine HS (Big Foot, TX) |
| 1999 | 39 | | 1182 | FrRnd | 18 | Cardinals | Monte Lee (minors) | | | | | | | | | | | | | 4Yr | College of Charleston (Charleston, SC) |
| 1999 | 39 | | 1183 | FrRnd | 19 | Blue Jays | Wilton Reynolds (minors) | | | | | | | | | | | | | JC | Cosumnes River College (Sacramento, CA) |
| 1999 | 40 | | 1201 | FrRnd | 7 | Royals | Jason Fransz (minors) | | | | | | | | | | | | | HS | Arlington HS (Riverside, CA) |
| 1999 | 40 | | 1206 | FrRnd | 12 | Phillies | Lawrence Alexander (minors) | | | | | | | | | | | | | HS | Chandler HS (Chandler, OK) |
| 1999 | 40 | | 1209 | FrRnd | 15 | White Sox | Jeremy Castillo (minors) | | | | | | | | | | | | | HS | Miami Southridge Sr HS (Miami, FL) |
| 1999 | 40 | | 1216 | FrRnd | 22 | Mets | Cory Harris (minors) | | | | | | | | | | | | | JC | Pensacola Junior College (Pensacola, FL) |
| 1999 | 40 | | 1219 | FrRnd | 25 | Red Sox | Anthony Bass (minors) | | | | | | | | | | | | | HS | Booker T. Washington HS (Tulsa, OK) |
| 1999 | 40 | | 1220 | FrRnd | 26 | Cubs | Justin Valenti (minors) | | | | | | | | | | | | | JC | Norwalk Community College (Norwalk, CT) |
| 1999 | 41 | | 1225 | FrRnd | 1 | Devil Rays | Glenn Katz (minors) | | | | | | | | | | | | | 4Yr | University of Connecticut (Storrs, CT) |
| 1999 | 41 | | 1231 | FrRnd | 7 | Royals | Herman Wright (minors) | | | | | | | | | | | | | HS | Odem HS (Odem, TX) |
| 1999 | 41 | | 1241 | FrRnd | 17 | Angels | Brandon Martin (minors) | | | | | | | | | | | | | JC | Riverside Community College (Riverside, CA) |
| 1999 | 41 | | 1242 | FrRnd | 18 | Blue Jays | Jeffrey Flegler (minors) | | | | | | | | | | | | | | |
| 1999 | 41 | | 1243 | FrRnd | 19 | Dodgers | Keith Godbolt (minors) | | | | | | | | | | | | | HS | Hillsborough HS (Tampa, FL) |
| 1999 | 41 | | 1247 | FrRnd | 23 | Giants | Winston Woods (minors) | | | | | | | | | | | | | JC | Broward Community College (Fort Lauderdale, FL) |
| 1999 | 41 | | 1249 | FrRnd | 25 | Cubs | Beau Benton (minors) | | | | | | | | | | | | | JC | Central Florida Community College (Ocala, FL) |
| 1999 | 41 | | 1250 | FrRnd | 26 | Yankees | Rob Garibaldi (minors) | | | | | | | | | | | | | JC | Santa Rosa Junior College (Santa Rosa, CA) |
| 1999 | 42 | | 1253 | FrRnd | 1 | Devil Rays | Ben Himes (minors) | | | | | | | | | | | | | HS | Westlake HS (Austin, TX) |
| 1999 | 42 | | 1255 | FrRnd | 3 | Tigers | Pete Pirman (minors) | | | | | | | | | | | | | JC | Triton College (River Grove, IL) |
| 1999 | 42 | | 1258 | FrRnd | 6 | Expos | Grant Oltjenbruns (minors) | | | | | | | | | | | | | JC | Fresno City College (Fresno, CA) |
| 1999 | 42 | | 1263 | FrRnd | 11 | Mariners | Tyson Munn (minors) | | | | | | | | | | | | | HS | Earl Marriott SS (Surrey, BC) |
| 1999 | 42 | | 1264 | FrRnd | 12 | Phillies | Erick Rivera (minors) | | | | | | | | | | | | | HS | Luis Munoz Marin HS (Yauco, PR) |
| 1999 | 42 | | 1266 | FrRnd | 14 | Reds | Bryan Erstad (minors) | | | | | | | | | | | | | HS | Jamestown HS (Jamestown, ND) |
| 1999 | 42 | | 1272 | FrRnd | 20 | Rangers | Adam Poe (minors) | | | | | | | | | | | | | 4Yr | University of South Carolina (Columbia, SC) |
| 1999 | 42 | | 1273 | FrRnd | 21 | Mets | Darius Shelby (minors) | | | | | | | | | | | | | HS | Valley View HS (Moreno Valley, CA) |
| 1999 | 43 | | 1284 | FrRnd | 5 | Twins | Bryan Williamson (minors) | | | | | | | | | | | | | 4Yr | University of Washington (Seattle, WA) |
| 1999 | 43 | | 1301 | FrRnd | 22 | Indians | Bradley Harrison (minors) | | | | | | | | | | | | | HS | Mandarin Sr HS (Jacksonville, FL) |
| 1999 | 44 | | 1328 | FrRnd | 22 | Indians | Mike Bishop (minors) | | | | | | | | | | | | | 4Yr | Kansas State University (Manhattan, KS) |
| 1999 | 44 | | 1330 | FrRnd | 24 | Red Sox | James Lindsey (minors) | | | | | | | | | | | | | HS | Lee Davis HS (Mechanicsville, VA) |
| 1999 | 44 | | 1332 | FrRnd | 26 | Yankees | Jeremiah Porter (minors) | | | | | | | | | | | | | HS | Columbia River HS (Vancouver, WA) |
| 1999 | 45 | | 1334 | FrRnd | 1 | Devil Rays | Chad Coder (minors) | | | | | | | | | | | | | HS | Eastlake HS (Sammamish, WA) |
| 1999 | 45 | | 1338 | FrRnd | 5 | Expos | Christopher Richard (minors) | | | | | | | | | | | | | JC | Norwalk Community College (Norwalk, CT) |
| 1999 | 45 | | 1341 | FrRnd | 8 | Athletics | William Zeier (minors) | | | | | | | | | | | | | JC | Laney College (Oakland, CA) |
| 1999 | 45 | | 1348 | FrRnd | 15 | Angels | Bill Curtis (minors) | | | | | | | | | | | | | 4Yr | Grand Canyon University (Phoenix, AZ) |
| 1999 | 45 | | 1351 | FrRnd | 18 | Rangers | Brad Hertel (minors) | | | | | | | | | | | | | HS | Clovis West HS (Fresno, CA) |
| 1999 | 45 | | 1356 | FrRnd | 23 | Cubs | Justin Sims (minors) | | | | | | | | | | | | | HS | Karns HS (Knoxville, TN) |
| 1999 | 46 | | 1371 | FrRnd | 13 | Rockies | T.J. Bird (minors) | | | | | | | | | | | | | JC | Mendocino College (Ukiah, CA) |
| 1999 | 46 | | 1372 | FrRnd | 14 | Angels | George Malone (minors) | | | | | | | | | | | | | HS | Victor Valley HS (Victorville, CA) |
| 1999 | 46 | | 1376 | FrRnd | 18 | Mets | Aaron Gureckis (minors) | | | | | | | | | | | | | HS | Nashua HS (Nashua, NH) |
| 1999 | 47 | | 1384 | FrRnd | 2 | Marlins | Jacob Robertson (minors) | | | | | | | | | | | | | HS | Twin Falls HS (Twin Falls, ID) |
| 1999 | 47 | | 1385 | FrRnd | 3 | Diamondbacks | Chris Jorgenson (minors) | | | | | | | | | | | | | HS | McCoy HS (New Brigden, AB) |
| 1999 | 47 | | 1387 | FrRnd | 5 | Expos | Matt Romero (minors) | | | | | | | | | | | | | JC | Utah Valley State University (Orem, UT) |
| 1999 | 47 | | 1389 | FrRnd | 7 | Pirates | Bryce Morrison (minors) | | | | | | | | | | | | | HS | Leander HS (Leander, TX) |
| 1999 | 47 | | 1393 | FrRnd | 11 | Reds | Leon Smith (minors) | | | | | | | | | | | | | HS | Greenbrier HS (Evans, GA) |
| 1999 | 47 | | 1403 | FrRnd | 21 | Red Sox | James Burgess (minors) | | | | | | | | | | | | | HS | Durango HS (Las Vegas, NV) |
| 1999 | 48 | | 1408 | FrRnd | 2 | Marlins | Quian Davis (minors) | | | | | | | | | | | | | HS | Buena Regional HS (Buena, NJ) |
| 1999 | 48 | | 1409 | FrRnd | 3 | Diamondbacks | Keith Schuttler (minors) | | | | | | | | | | | | | HS | Agua Fria HS (Avondale, AZ) |
| 1999 | 48 | | 1414 | FrRnd | 8 | Brewers | Amos Burgess (minors) | | | | | | | | | | | | | HS | Lone Peak HS (Alpine, UT) |
| 1999 | 48 | | 1419 | FrRnd | 13 | Rockies | Manases Pabon (minors) | | | | | | | | | | | | | JC | Indian Hills Community College (Centerville, IA) |
| 1999 | 48 | | 1421 | FrRnd | 15 | Blue Jays | Jon Slack (minors) | | | | | | | | | | | | | HS | Green Valley HS (Henderson, NV) |
| 1999 | 48 | | 1424 | FrRnd | 18 | Mets | Vincent White (minors) | | | | | | | | | | | | | JC | John Abbott College (Beaconsfield, QC) |
| 1999 | 49 | | 1431 | FrRnd | 1 | Devil Rays | Randy Walter (minors) | | | | | | | | | | | | | HS | Huntley Project HS (Ballantine, MT) |
| 1999 | 49 | | 1436 | FrRnd | 6 | Pirates | Brian Pollard (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 1999 | 49 | | 1437 | FrRnd | 7 | Brewers | Blair Bourque (minors) | | | | | | | | | | | | | HS | Taunton HS (Taunton, MA) |
| 1999 | 49 | | 1441 | FrRnd | 11 | White Sox | Austin Rappe (minors) | | | | | | | | | | | | | 4Yr | Virginia Polytechnic Institute and State University (Blacksburg, VA) |
| 1999 | 49 | | 1446 | FrRnd | 16 | Rangers | Nathan Neibauer (minors) | | | | | | | | | | | | | HS | Overland HS (Aurora, CO) |
| 1999 | 49 | | 1447 | FrRnd | 17 | Mets | Eric Bernier (minors) | | | | | | | | | | | | | HS | Cegep Edouard Monpetit HS (Montreal, QC) |
| 1999 | 49 | | 1448 | FrRnd | 18 | Indians | Neal Maybin (minors) | | | | | | | | | | | | | JC | Brevard Community College (Cocoa, FL) |
| 1999 | 49 | | 1451 | FrRnd | 21 | Cubs | Ryan Johnson (minors) | | | | | | | | | | | | | HS | Laguna Hills HS (Laguna Hills, CA) |
| 1999 | 50 | | 1455 | FrRnd | 2 | Marlins | Anthony Aceves (minors) | | | | | | | | | | | | | HS | Howard HS (Columbia, MD) |
| 1999 | 50 | | 1456 | FrRnd | 3 | Diamondbacks | Peter Hawley (minors) | | | | | | | | | | | | | HS | Branford HS (Branford, CT) |
| 1999 | 50 | | 1457 | FrRnd | 4 | Twins | Joseph Ammirato (minors) | | | | | | | | | | | | | HS | Marina HS (Huntington Beach, CA) |
| 1999 | 50 | | 1458 | FrRnd | 5 | Royals | Byron Russell (minors) | | | | | | | | | | | | | HS | Pamplico County HS (Bayboro, NC) |
| 1999 | 50 | | 1467 | FrRnd | 14 | Rangers | Clay Chesser (minors) | | | | | | | | | | | | | HS | Golden West HS (Visalia, CA) |
| 1999 | 50 | | 1470 | FrRnd | 17 | Giants | Bryan Grochol (minors) | | | | | | | | | | | | | JC | Canada College (Redwood City, CA) |