| 2012 | 1 | | 1 | FrRnd | 1 | Astros | Carlos Correa (minors) | | | | | | | | | | | | | HS | Puerto Rico Baseball Academy (Gurabo, PR) |
| 2012 | 1 | | 11 | FrRnd | 11 | Athletics | Addison Russell (minors) | | | | | | | | | | | | | HS | Pace HS (Pace, FL) |
| 2012 | 1 | | 12 | FrRnd | 12 | Mets | Gavin Cecchini (minors) | | | | | | | | | | | | | HS | Alfred M. Barbe HS (Lake Charles, LA) |
| 2012 | 1 | | 18 | FrRnd | 18 | Dodgers | Corey Seager (minors) | | | | | | | | | | | | | HS | Northwest Cabarrus HS (Concord, NC) |
| 2012 | 1 | | 24 | FrRnd | 24 | Red Sox | Deven Marrero (minors) | | | | | | | | | | | | | 4Yr | Arizona State University (Tempe, AZ) |
| 2012 | 1s | | 34 | FrRnd | 34 | Athletics | *Daniel Robertson (minors) | | | | | | | | | | | | | HS | Upland HS (Upland, CA) |
| 2012 | 1s | | 51 | FrRnd | 51 | Dodgers | *Jesmuel Valentin (minors) | | | | | | | | | | | | | HS | Puerto Rico Baseball Academy (Gurabo, PR) |
| 2012 | 2 | | 61 | FrRnd | 1 | Astros | Nolan Fontana (minors) | | | | | | | | | | | | | 4Yr | University of Florida (Gainesville, FL) |
| 2012 | 2 | | 64 | FrRnd | 4 | Mariners | Joe DeCarlo (minors) | | | | | | | | | | | | | HS | Garnet Valley HS (Glen Mills, PA) |
| 2012 | 2 | | 78 | FrRnd | 18 | Reds | Tanner Rahier (minors) | | | | | | | | | | | | | HS | Palm Desert HS (Palm Desert, CA) |
| 2012 | 2 | | 88 | FrRnd | 28 | Rays | Spencer Edwards (minors) | | | | | | | | | | | | | HS | Rockwall HS (Rockwall, TX) |
| 2012 | 2 | | 90 | FrRnd | 30 | Diamondbacks | Jose Munoz (minors) | | | | | | | | | | | | | HS | Los Altos HS (Hacienda Heights, CA) |
| 2012 | 3 | | 99 | FrRnd | 4 | Orioles | Adrian Marin (minors) | | | | | | | | | | | | | HS | Gulliver Prep (Miami, FL) |
| 2012 | 3 | | 102 | FrRnd | 7 | Padres | Fernando Perez (minors) | | | | | | | | | | | | | JC | Central Arizona College (Coolidge, AZ) |
| 2012 | 3 | | 104 | FrRnd | 9 | Marlins | Avery Romero (minors) | | | | | | | | | | | | | HS | Pedro Menendez HS (St. Augustine, FL) |
| 2012 | 3 | | 125 | FrRnd | 30 | Phillies | Zach Green (minors) | | | | | | | | | | | | | HS | Jesuit HS (Sacramento, CA) |
| 2012 | 4 | | 133 | FrRnd | 5 | Royals | Kenny Diekroeger (minors) | | | | | | | | | | | | | 4Yr | Stanford University (Palo Alto, CA) |
| 2012 | 4 | | 140 | FrRnd | 12 | Mets | Branden Kaupe (minors) | | | | | | | | | | | | | HS | Baldwin HS (Wailuku, HI) |
| 2012 | 4 | | 150 | FrRnd | 22 | Cardinals | Alex Mejia (minors) | | | | | | | | | | | | | 4Yr | University of Arizona (Tucson, AZ) |
| 2012 | 5 | | 161 | FrRnd | 3 | Mariners | Chris Taylor (minors) | | | | | | | | | | | | | 4Yr | University of Virginia (Charlottesville, VA) |
| 2012 | 5 | | 167 | FrRnd | 9 | Marlins | Austin Nola (minors) | | | | | | | | | | | | | 4Yr | Louisiana State University (Baton Rouge, LA) |
| 2012 | 5 | | 168 | FrRnd | 10 | Rockies | Matt Wessinger (minors) | | | | | | | | | | | | | 4Yr | St. John's University (Queens, NY) |
| 2012 | 5 | | 171 | FrRnd | 13 | White Sox | Nick Basto (minors) | | | | | | | | | | | | | HS | Archbishop McCarthy HS (Southwest Ranches, FL) |
| 2012 | 6 | | 191 | FrRnd | 3 | Mariners | Timmy Lopes (minors) | | | | | | | | | | | | | HS | Edison HS (Huntington Beach, CA) |
| 2012 | 6 | | 195 | FrRnd | 7 | Padres | Jalen Goree (minors) | | | | | | | | | | | | | HS | Bibb County HS (Centreville, AL) |
| 2012 | 6 | | 197 | FrRnd | 9 | Marlins | Anthony Gomez (minors) | | | | | | | | | | | | | 4Yr | Vanderbilt University (Nashville, TN) |
| 2012 | 6 | | 207 | FrRnd | 19 | Angels | Eric Stamets (minors) | | | | | | | | | | | | | 4Yr | University of Evansville (Evansville, IN) |
| 2012 | 6 | | 215 | FrRnd | 27 | Brewers | Angel Ortega (minors) | | | | | | | | | | | | | HS | International Baseball Academy (Ceiba, PR) |
| 2012 | 7 | | 243 | FrRnd | 25 | Diamondbacks | Andrew Velazquez (minors) | | | | | | | | | | | | | HS | Fordham Prep HS (New York, NY) |
| 2012 | 8 | | 256 | FrRnd | 8 | Pirates | Kevin Ross (minors) | | | | | | | | | | | | | HS | Niles West HS (Skokie, IL) |
| 2012 | 8 | | 264 | FrRnd | 16 | Nationals | Stephen Perez (minors) | | | | | | | | | | | | | 4Yr | University of Miami (Coral Gables, FL) |
| 2012 | 9 | | 286 | FrRnd | 8 | Pirates | D.J. Crumlich (minors) | | | | | | | | | | | | | 4Yr | University of California, Irvine (Irvine, CA) |
| 2012 | 9 | | 301 | FrRnd | 23 | Red Sox | Mike Miller (minors) | | | | | | | | | | | | | 4Yr | California Polytechnic State University, San Luis Obispo (San Luis Obispo, CA) |
| 2012 | 10 | | 312 | FrRnd | 4 | Orioles | Joel Hutter (minors) | | | | | | | | | | | | | 4Yr | Dallas Baptist University (Dallas, TX) |
| 2012 | 10 | | 315 | FrRnd | 7 | Padres | Stephen Carmon (minors) | | | | | | | | | | | | | 4Yr | University of South Carolina Aiken (Aiken, SC) |
| 2012 | 11 | | 346 | FrRnd | 8 | Pirates | Chris Diaz (minors) | | | | | | | | | | | | | 4Yr | North Carolina State University (Raleigh, NC) |
| 2012 | 11 | | 349 | FrRnd | 11 | Athletics | Matt Gonzalez (minors) | | | | | | | | | | | | | HS | Harrison HS (Kennesaw, GA) |
| 2012 | 11 | | 360 | FrRnd | 22 | Cardinals | Trey Williams (minors) | | | | | | | | | | | | | HS | Valencia HS (Valencia, CA) |
| 2012 | 12 | | 377 | FrRnd | 9 | Marlins | Christian Rivera (minors) | | | | | | | | | | | | | HS | Escuela Nueva Superior Vocacional de Loiza (Loiza, PR) |
| 2012 | 12 | | 382 | FrRnd | 14 | Reds | Brent Peterson (minors) | | | | | | | | | | | | | JC | Bakersfield College (Bakersfield, CA) |
| 2012 | 12 | | 388 | FrRnd | 20 | Giants | Jeremy Sy (minors) | | | | | | | | | | | | | 4Yr | University of Louisiana at Monroe (Monroe, LA) |
| 2012 | 12 | | 391 | FrRnd | 23 | Red Sox | Mike Meyers (minors) | | | | | | | | | | | | | HS | Silverado HS (Las Vegas, NV) |
| 2012 | 13 | | 416 | FrRnd | 18 | Dodgers | Darnell Sweeney (minors) | | | | | | | | | | | | | 4Yr | University of Central Florida (Orlando, FL) |
| 2012 | 13 | | 420 | FrRnd | 22 | Cardinals | Brett Wiley (minors) | | | | | | | | | | | | | JC | Jefferson College (Hillsboro, MO) |
| 2012 | 14 | | 429 | FrRnd | 1 | Astros | Joe Sclafani (minors) | | | | | | | | | | | | | 4Yr | Dartmouth College (Hanover, NH) |
| 2012 | 14 | | 450 | FrRnd | 22 | Cardinals | Anthony Melchionda (minors) | | | | | | | | | | | | | 4Yr | Boston College (Chestnut Hill, MA) |
| 2012 | 15 | | 480 | FrRnd | 22 | Cardinals | Bruce Caldwell (minors) | | | | | | | | | | | | | JC | Spartanburg Methodist College (Spartanburg, SC) |
| 2012 | 15 | | 484 | FrRnd | 26 | Tigers | Jordan Dean (minors) | | | | | | | | | | | | | 4Yr | Central Michigan University (Mount Pleasant, MI) |
| 2012 | 16 | | 490 | FrRnd | 2 | Twins | Will Hurt (minors) | | | | | | | | | | | | | HS | Lexington Catholic HS (Lexington, KY) |
| 2012 | 16 | | 496 | FrRnd | 8 | Pirates | Max Moroff (minors) | | | | | | | | | | | | | HS | Trinity Prep School (Winter Park, FL) |
| 2012 | 16 | | 499 | FrRnd | 11 | Athletics | Melvin Mercedes (minors) | | | | | | | | | | | | | 4Yr | University of Central Florida (Orlando, FL) |
| 2012 | 16 | | 513 | FrRnd | 25 | Diamondbacks | Landon Lassiter (minors) | | | | | | | | | | | | | HS | North Davidson HS (Lexington, NC) |
| 2012 | 17 | | 528 | FrRnd | 10 | Rockies | Jason Stolz (minors) | | | | | | | | | | | | | 4Yr | Clemson University (Clemson, SC) |
| 2012 | 17 | | 542 | FrRnd | 24 | Rays | Ryan Dunn (minors) | | | | | | | | | | | | | 4Yr | Oregon State University (Corvallis, OR) |
| 2012 | 17 | | 545 | FrRnd | 27 | Brewers | Alfredo Rodriguez (minors) | | | | | | | | | | | | | 4Yr | University of Maryland (College Park, MD) |
| 2012 | 18 | | 554 | FrRnd | 6 | Cubs | David Bote (minors) | | | | | | | | | | | | | JC | Neosho County Community College (Chanute, KS) |
| 2012 | 18 | | 568 | FrRnd | 20 | Giants | Matthew Duffy (minors) | | | | | | | | | | | | | 4Yr | California State University Long Beach (Long Beach, CA) |
| 2012 | 19 | | 595 | FrRnd | 17 | Blue Jays | Jorge Flores (minors) | | | | | | | | | | | | | JC | Central Arizona College (Coolidge, AZ) |
| 2012 | 19 | | 601 | FrRnd | 23 | Red Sox | Iseha Conklin (minors) | | | | | | | | | | | | | JC | Iowa Western Community College (Council Bluffs, IA) |
| 2012 | 19 | | 608 | FrRnd | 30 | Phillies | Tim Carver (minors) | | | | | | | | | | | | | 4Yr | University of Arkansas (Fayetteville, AR) |
| 2012 | 20 | | 621 | FrRnd | 13 | White Sox | Zachary Voight (minors) | | | | | | | | | | | | | 4Yr | New Mexico State University (Las Cruces, NM) |
| 2012 | 20 | | 624 | FrRnd | 16 | Nationals | James Brooks (minors) | | | | | | | | | | | | | 4Yr | University of Utah (Salt Lake City, UT) |
| 2012 | 20 | | 629 | FrRnd | 21 | Braves | Eric Garcia (minors) | | | | | | | | | | | | | 4Yr | University of Missouri Columbia (Columbia, MO) |
| 2012 | 20 | | 635 | FrRnd | 27 | Brewers | Mike Garza (minors) | | | | | | | | | | | | | 4Yr | Georgetown University (Washington, DC) |
| 2012 | 20 | | 637 | FrRnd | 29 | Yankees | Michael Reynolds (minors) | | | | | | | | | | | | | 4Yr | Texas A&M University (College Station, TX) |
| 2012 | 22 | | 671 | FrRnd | 3 | Mariners | Gabrial Franca (minors) | | | | | | | | | | | | | HS | John North HS (Riverside, CA) |
| 2012 | 23 | | 715 | FrRnd | 17 | Blue Jays | Trey Pascazi (minors) | | | | | | | | | | | | | HS | East Rochester HS (East Rochester, NY) |
| 2012 | 24 | | 729 | FrRnd | 1 | Astros | Patrick Blair (minors) | | | | | | | | | | | | | 4Yr | Wake Forest University (Winston-Salem, NC) |
| 2012 | 25 | | 759 | FrRnd | 1 | Astros | Ryan Dineen (minors) | | | | | | | | | | | | | 4Yr | Eastern Illinois University (Charleston, IL) |
| 2012 | 25 | | 768 | FrRnd | 10 | Rockies | Alec Mehrten (minors) | | | | | | | | | | | | | 4Yr | Fresno Pacific University (Fresno, CA) |
| 2012 | 25 | | 775 | FrRnd | 17 | Blue Jays | Jason Leblebijian (minors) | | | | | | | | | | | | | 4Yr | Bradley University (Peoria, IL) |
| 2012 | 25 | | 784 | FrRnd | 26 | Tigers | Jared Reaves (minors) | | | | | | | | | | | | | 4Yr | University of Alabama (Tuscaloosa, AL) |
| 2012 | 25 | | 786 | FrRnd | 28 | Rangers | Gabriel Roa (minors) | | | | | | | | | | | | | JC | Wabash Valley College (Mount Carmel, IL) |
| 2012 | 26 | | 789 | FrRnd | 1 | Astros | C.J. Hinojosa (minors) | | | | | | | | | | | | | HS | Klein Collins HS (Spring, TX) |
| 2012 | 27 | | 822 | FrRnd | 4 | Orioles | Anthony Caronia (minors) | | | | | | | | | | | | | 4Yr | University of Tampa (Tampa, FL) |
| 2012 | 27 | | 836 | FrRnd | 18 | Dodgers | Justin Gonzalez (minors) | | | | | | | | | | | | | 4Yr | Florida State University (Tallahassee, FL) |
| 2012 | 28 | | 864 | FrRnd | 16 | Nationals | Hunter Bailey (minors) | | | | | | | | | | | | | 4Yr | Oklahoma State University (Stillwater, OK) |
| 2012 | 28 | | 869 | FrRnd | 21 | Braves | K.C. Clabough (minors) | | | | | | | | | | | | | 4Yr | Florida Institute of Technology (Melbourne, FL) |
| 2012 | 28 | | 873 | FrRnd | 25 | Diamondbacks | Max Schrock (minors) | | | | | | | | | | | | | HS | Cardinal Gibbons HS (Raleigh, NC) |
| 2012 | 29 | | 897 | FrRnd | 19 | Angels | Caleb Bushyhead (minors) | | | | | | | | | | | | | 4Yr | University of Oklahoma (Norman, OK) |
| 2012 | 29 | | 903 | FrRnd | 25 | Diamondbacks | Adam McConnell (minors) | | | | | | | | | | | | | 4Yr | University of Richmond (Richmond, VA) |
| 2012 | 30 | | 919 | FrRnd | 11 | Athletics | Christopher Wolfe (minors) | | | | | | | | | | | | | 4Yr | Grambling State University (Grambling, LA) |
| 2012 | 30 | | 921 | FrRnd | 13 | White Sox | Jake Brown (minors) | | | | | | | | | | | | | 4Yr | Kansas State University (Manhattan, KS) |
| 2012 | 30 | | 923 | FrRnd | 15 | Indians | Josh Lester (minors) | | | | | | | | | | | | | HS | Columbus HS (Columbus, GA) |
| 2012 | 30 | | 926 | FrRnd | 18 | Dodgers | Trent Giambrone (minors) | | | | | | | | | | | | | HS | Grace King HS (Metairie, LA) |
| 2012 | 31 | | 947 | FrRnd | 9 | Marlins | Lucas Hunter (minors) | | | | | | | | | | | | | HS | Central Catholic HS (Portland, OR) |
| 2012 | 31 | | 950 | FrRnd | 12 | Mets | Vance Vizcaino (minors) | | | | | | | | | | | | | HS | Wakefield HS (Raleigh, NC) |
| 2012 | 31 | | 955 | FrRnd | 17 | Blue Jays | Derrick Chung (minors) | | | | | | | | | | | | | 4Yr | California State University Sacramento (Sacramento, CA) |
| 2012 | 31 | | 957 | FrRnd | 19 | Angels | Jeff Kemp (minors) | | | | | | | | | | | | | 4Yr | Radford University (Radford, VA) |
| 2012 | 32 | | 974 | FrRnd | 6 | Cubs | Tim Saunders (minors) | | | | | | | | | | | | | 4Yr | Marietta College (Marietta, OH) |
| 2012 | 32 | | 978 | FrRnd | 10 | Rockies | Austin Simcox (minors) | | | | | | | | | | | | | HS | Farragut HS (Knoxville, TN) |
| 2012 | 32 | | 983 | FrRnd | 15 | Indians | Paul Hendrix (minors) | | | | | | | | | | | | | JC | Howard College (Big Spring, TX) |
| 2012 | 32 | | 990 | FrRnd | 22 | Cardinals | Eduardo Oquendo (minors) | | | | | | | | | | | | | JC | Olney Central College (Olney, IL) |
| 2012 | 32 | | 992 | FrRnd | 24 | Rays | Ben Kline (minors) | | | | | | | | | | | | | 4Yr | Embry-Riddle Aeronautical University (Daytona Beach, FL) |
| 2012 | 32 | | 997 | FrRnd | 29 | Yankees | Garrett Cannizaro (minors) | | | | | | | | | | | | | 4Yr | Tulane University (New Orleans, LA) |
| 2012 | 33 | | 1013 | FrRnd | 15 | Indians | Cory Raley (minors) | | | | | | | | | | | | | HS | Uvalde HS (Uvalde, TX) |
| 2012 | 34 | | 1039 | FrRnd | 11 | Athletics | Devon Gradford (minors) | | | | | | | | | | | | | HS | Downey HS (Modesto, CA) |
| 2012 | 34 | | 1040 | FrRnd | 12 | Mets | Mikey White (minors) | | | | | | | | | | | | | HS | Spain Park HS (Hoover, AL) |
| 2012 | 34 | | 1045 | FrRnd | 17 | Blue Jays | Brandon Lopez (minors) | | | | | | | | | | | | | HS | American Heritage HS (Plantation, FL) |
| 2012 | 35 | | 1061 | FrRnd | 3 | Mariners | Tyler Krieger (minors) | | | | | | | | | | | | | HS | Northview HS (Johns Creek, GA) |
| 2012 | 35 | | 1073 | FrRnd | 15 | Indians | Nick Hamilton (minors) | | | | | | | | | | | | | 4Yr | Kent State University (Kent, OH) |
| 2012 | 35 | | 1079 | FrRnd | 21 | Braves | Matt Creech (minors) | | | | | | | | | | | | | HS | Colquitt County HS (Moultrie, GA) |
| 2012 | 35 | | 1085 | FrRnd | 27 | Brewers | Jose Sermo (minors) | | | | | | | | | | | | | 4Yr | Bethany College (Lindsborg, KS) |
| 2012 | 35 | | 1087 | FrRnd | 29 | Yankees | Kyle Farmer (minors) | | | | | | | | | | | | | 4Yr | University of Georgia (Athens, GA) |
| 2012 | 36 | | 1098 | FrRnd | 10 | Rockies | Kevin Bradley (minors) | | | | | | | | | | | | | HS | Hopewell Valley Central HS (Pennington, NJ) |
| 2012 | 36 | | 1100 | FrRnd | 12 | Mets | Donovan Walton (minors) | | | | | | | | | | | | | HS | Bishop Kelley HS (Tulsa, OK) |
| 2012 | 36 | | 1105 | FrRnd | 17 | Blue Jays | Brian Cruz (minors) | | | | | | | | | | | | | JC | Galveston College (Galveston, TX) |
| 2012 | 36 | | 1106 | FrRnd | 18 | Dodgers | Jose Vizcaino (minors) | | | | | | | | | | | | | HS | Parker HS (San Diego, CA) |
| 2012 | 36 | | 1112 | FrRnd | 24 | Rays | Brett McAfee (minors) | | | | | | | | | | | | | JC | Panola College (Carthage, TX) |
| 2012 | 37 | | 1132 | FrRnd | 14 | Reds | Zach Vincej (minors) | | | | | | | | | | | | | 4Yr | Pepperdine University (Malibu, CA) |
| 2012 | 37 | | 1138 | FrRnd | 20 | Giants | Drew Jackson (minors) | | | | | | | | | | | | | HS | Miramonte HS (Orinda, CA) |
| 2012 | 37 | | 1145 | FrRnd | 27 | Brewers | Taylor Smith-Brennan (minors) | | | | | | | | | | | | | JC | Edmonds Community College (Lynnwood, WA) |
| 2012 | 38 | | 1151 | FrRnd | 3 | Mariners | Richard Martin (minors) | | | | | | | | | | | | | HS | Bloomingdale HS (Bloomingdale, FL) |
| 2012 | 38 | | 1155 | FrRnd | 7 | Padres | Adam Ford (minors) | | | | | | | | | | | | | HS | Trousdale County HS (Hartsville, TN) |
| 2012 | 38 | | 1158 | FrRnd | 10 | Rockies | Dansby Swanson (minors) | | | | | | | | | | | | | HS | Marietta HS (Marietta, GA) |
| 2012 | 38 | | 1161 | FrRnd | 13 | White Sox | DeJohn Suber (minors) | | | | | | | | | | | | | HS | Morgan Park HS (Chicago, IL) |
| 2012 | 38 | | 1165 | FrRnd | 17 | Blue Jays | Nick Lovullo (minors) | | | | | | | | | | | | | HS | Newbury Park HS (Thousand Oaks, CA) |
| 2012 | 39 | | 1204 | FrRnd | 26 | Tigers | John Sansone (minors) | | | | | | | | | | | | | HS | Neshannock HS (Neshannock, PA) |
| 2012 | 40 | | 1217 | FrRnd | 9 | Marlins | Alex Polston (minors) | | | | | | | | | | | | | HS | Carl Albert HS (Midwest City, OK) |
| 2012 | 40 | | 1219 | FrRnd | 11 | Athletics | David Olmedo-Barrera (minors) | | | | | | | | | | | | | HS | St. Francis HS (Mountain View, CA) |
| 2012 | 40 | | 1225 | FrRnd | 17 | Blue Jays | Jose Cuas (minors) | | | | | | | | | | | | | HS | Grand Street Campus (Brooklyn, NY) |