The scandal first broke out on January 29, 2013 when the Miami New Times reported that the clinic had sold various illegal substances to a number of prominent athletes, including many baseball players. It stated a number of names of those suspected of having been clients, among them Alex Rodriguez, around whom rumors of illegal PED use had been rampant for a number of years, in addition to three players who had all recently been suspended for violating MLB's drug testing and treatment program, Bartolo Colon, Yasmani Grandal and Melky Cabrera, and a fourth - Ryan Braun - who had only avoided such a suspension when arbitrator Shyam Das ruled that MLB had not followed procedure in handling Braun's urine sample. A number of heretofore untainted players were also mentioned, such as Nelson Cruz, Gio Gonzalez and Everth Cabrera. MLB responded by stating that it would cooperate fully with Federal authorities investigating the matter and launch its own probe.
The New Times investigation uncovered the fact that the clinic's principal, Anthony "Tony" Bosch, was a professional huckster with a fake medical degree. The clinic was located near the University of Miami campus and it seems that its links to a clientele numbering some top athletes (not only baseball players) went through that institution's athletics program. Most of the players fingered were clients of the ACES sports agency, with one particular employee, Juan Carlos Nunez, being identified as the go-between between Bosch and his baseball clientele; the agency's principal, Seth Levinson, claimed that ACES management was not aware of Nunez's activities and described him as a "rogue employee". Nunez had been fired in August of 2012 for his role in trying to cover up Melky Cabrera's positive test. Biogenesis had closed abruptly in December of 2012, and Bosch seemingly disappeared shortly after a clinic employee provided the newspaper with incriminating evidence about its activities. The documents showed clearly that the business was a front for selling Human Growth Hormone, anabolic steroids and testosterone to top-notch athletes. Bosch had already featured in a previous baseball drug case, as the person who had sold Manny Ramirez the substances that led to his suspension in 2009.
Over the next few months, MLB interviewed all of the players whose names had turned up in the clinic's records and, in a controversial step, bought some documents from the clinic to further its investigation. The testimony from Tony Bosch affirmed initial suspicions. The first penalty was handed down on July 22nd, when Ryan Braun agreed not to contest the evidence against him and accept a suspension for the remainder of the season - equivalent to 65 games.
On August 5th, MLB announced 50-game suspensions for Everth Cabrera, Francisco Cervelli, Nelson Cruz, Jesus Montero, Jhonny Peralta, Antonio Bastardo and Jordany Valdespin, and minor leaguers Sergio Escalona, Fautino De Los Santos, Fernando Martinez, Jordan Norberto and Cesar Puello. Bartolo Colon, Yasmani Grandal and Melky Cabrera were not suspended as their previous suspensions for positive tests during the range of time the investigation covered meant that suspending them again could constitute double jeopardy. Alex Rodriguez was suspended for the balance of the 2013 season and the end of the 2014 regular season. However, Rodriguez, alone among the 13, decided to appeal his suspension, and ironically made his season's debut that very day, having been on the sidelines all year following off-season hip surgery. The investigation found no violations committed by Gio Gonzalez and Danny Valencia, whose names had also turned up during the investigation.
Public and media response to the BALCO and the Biogenesis scandals was quite different. Many fans and reporters had been incredulous of the allegations emerging from the BALCO investigation almost a decade earlier, claiming that either there was no evidence that PEDs had any measurable effect on performance, or that "everyone was doing it" and the few players caught were in effect scapegoats, or that the players were not aware of what products they had been taking. The latter argument was the line of defense used by Barry Bonds during his trial in 2011. However, after the Miami New Times article, polls of fans showed overwhelming numbers in favor of harsh penalties for drug offenders; tainted players had done extremely poorly in Hall of Fame voting, particularly in the so-called "steroid ballot" of 2013 which failed to elect anyone, and outside events such as the confession and public shaming of cyclist Lance Armstrong had only stoked the resentment against the "cheaters". Even among players, the mood had changed significantly: Michael Weiner, head of the Player's Union, was an outspoken opponent of PED use, and the number of prominent players willing to speak against their transgressing peers was growing quickly.
As part of the Major League Baseball Players Association's response to the announcement of suspensions and Rodriguez' appeal, Michael Weiner asserted that the MLBPA had concerns about the investigative leaks under the Joint-Drug Agreement's agreed upon confidential conditions. He expressed "profound disappointment in the way individuals granted access to private and privileged information felt compelled to share that information publicly. The manner in which confidential information was so freely exchanged is not only a threat to the success and credibility of our [Joint-Drug Agreement]; it calls into question the level of trust required to administer such a program. It is our view that when the bargaining parties hold their annual review of the program, we must revisit the JDA’s confidentiality provisions and consider implementing stricter rules for any breach by any individual involved in the process."
While the suspended players completed their sentence at the end of the 2013 season - two of them, Jhonny Peralta and Nelson Cruz, were even able to come back and play in the postseason, A-Rod's appeal was still ongoing after the season ended. After a series of hearings, arbitrator Fredric Horowitz, who had replaced Shyam Das, decided on January 11, 2014 to reduce Rodriguez's sentence to 162 games, or the full 2014 season and postseason. The MLBPA stated that it disagreed with the decision but would accept it, but A-Rod's clan immediately indicated it would now seek an appeal through federal court. The following day, a report aired on the televised news program 60 Minutes contained more damaging allegations against the fallen superstar, as Tony Bosch stated he had personally injected Rodriguez with banned substances, had guided him on how to avoid tests, and had even provided with testosterone-laced lozenges to take before games. Rodriguez's lawyers immediately denounced Bosch's statements as lies, while the MLBPA was unhappy that MLB Vice-President Rob Manfred had agreed to speak on camera to the show's reporters, in contradiction with the cooperation between the union and MLB from the time the scandal had broken out. Rodriguez made good on his threat to appeal the suspension on January 13th, when he filed a lawsuit in federal court in Manhattan against MLB and the MLBPA seeking to have the suspension overturned. However, he later dropped the suit, accepting his one-year suspension.
In August of 2014, Tony Bosch surrendered to federal authorities and agreed to face a number of charges of distributing steroids and other illegal substances and he pleaded guilty in October. He was hoping that his cooperation with MLB's enquiry would reduce considerably any potential sentence. A number of associates surrendered at the same time, leading to speculation that a second wave of names of alleged users would be made public as a result. That did not come about, but on February 17, 2015, Bosch was sentenced to four years in prison, Judge Darrin Gayles deciding not to show much leniency in spite of Bosch's cooperation with authorities. Gayles described Bosch as the mastermind of the operation and added that a stiff sentence was appropriate. Still, in January of 2016, Judge Gayle did reduce Bosch's sentence by 16 months at the request of prosecutors in reward for his extensive cooperation with authorities that had provided key evidence in at least four other cases.
- Tim Elfrink: "A Miami Clinic Supplies Drugs to Sports' Biggest Names", The Miami New Times, January 31, 2013. 
- Tim Elfrink and Gus Garcia-Roberts: Blood Sport: Alex Rodriguez, Biogenesis and the Quest to End Baseball's Steroid Era, Dutton, Penguin Books, New York, NY, 2014. ISBN 978-0525954637
- Bob Nightengale: "Biogenesis, a year later: MLB's joyless probe endures", USA Today, August 5, 2014. 
- Mike Oz: "Anthony Bosch gets four years in prison, despite MLB vouching for him", Big League Stew, Yahoo! Sports, February 17, 2015.