He was suspended and later reinstated by Churchill Downs following the use of the topical steroid cream betamethasone on his Kentucky Derby winner, Medina Spirit, who was subsequently disqualified.

Fellow trainer D. Wayne Lukas attributed Baffert's success to his "extraordinary eye for a good horse" and his management ability in finding the right opportunities for his charges.

[5] Baffert's history in the American Classic races began in 1996 when he trained a three-year-old colt named Cavonnier, who ran second in the Kentucky Derby.

Real Quiet won the Preakness as well, but, like Silver Charm, the horse was denied a Triple Crown win and finished second in the Belmont Stakes by a nose.

Baffert did not win another classic race until 2001, when he won the Preakness and Belmont Stakes with eventual Hall of Fame member Point Given.

Baffert did not have a horse hit the board again in any of the Triple Crown races until 2009, when he trained Pioneerof The Nile to a second-place finish in the Derby.

In winning the 141st Kentucky Derby, bringing his total number of victories in the race to four; Baffert also ran the third-place finisher, the previously undefeated colt Dortmund.

Medina Spirit's drug violation led to several racetracks suspending Baffert from entering races, including a ban of over three years by tracks owned by Churchill Downs.

In 2010, Misremembered, a horse he bred, owned by his wife Jill and their friend George Jacobs, won the Santa Anita Handicap, marking Baffert's first Grade I win as a breeder instead of a trainer.

In September 2019 The New York Times reported that Justify tested positive for the banned substance scopolamine after winning the Santa Anita Derby.

[13] After legal battles, in December 2023 a judge ordered stewards of the California Horse Racing Board to issue a new ruling which would effectively disqualify Justify from his win.

[23][24] Sports Illustrated suggested that the positive drug test was a sign that Baffert's "leaking credibility" had reached "the saturation point.

"[25] On June 2, 2021, Medina Spirit's split sample also tested positive and Churchill Downs suspended Baffert through the end of the 2023 Spring Meet.

[27][28] On June 14, 2021, Baffert sued the NYRA alleging the association had no authority to suspend his license and that suspension "without prior notice" was a violation of the law.

[37] The most notable cases prior to Medina Spirit's test were the disqualification of Gamine after a third-place finish in the 2020 Kentucky Oaks, also for betamethasone,[38] and Triple Crown winner Justify, who tested positive for scopolamine after winning the 2018 Santa Anita Derby, but the results did not become public until after the horse won the Triple Crown.

Similarly, cases against two horses who tested positive in Arkansas in 2020 for lidocaine were dismissed as being the result of accidental transfer from an assistant trainer who was using the medication on himself.

[10] Controversy deepened when on December 6, 2021, Medina Spirit died of an apparent heart attack after a workout at Santa Anita Park.

[11] Prior to Medina Spirit's death, Baffert had last been under intense scrutiny a decade earlier when seven horses in his stables at Hollywood Park died between November 2, 2011, and March 14, 2013, all from sudden and later unexplained heart attacks.

One year later, in July 2024, Churchill Downs rescinded the ban after Baffert issued a statement accepting responsibility for Medina Spirit's drug positive and for any substance found in the horses that he trained.

"I have paid a very steep price with a three-year suspension and the disqualification of Medina Spirit’s performance," he said, adding that he was "committed to having an amicable resolution with Churchill Downs in order to have the opportunity to compete again for the Triple Crown.

[47] At the post-Belmont press conference, Baffert announced he and his wife would be making donations of $50,000 each to the Thoroughbred Aftercare Alliance, the California Retirement Management Account (CARMA), and Old Friends Equine, all programs for retired race horses; and to the Permanently Disabled Jockey's Fund in memory of a Quarter Horse Jockey named Robert Z.

[46][48] A friend of Baffert's and an inductee into the American Quarter Horse Association Hall of Fame, Adair died on Preakness Day, May 16, 2015, at 71.