The Office of the Commissioner of Baseball said second baseman Ryan Brett and pitchers Charles Cononie and Justin Woodall each tested positive for methamphetamine and an amphetamine.
All three players have received 50-game suspensions without pay, effective immediately.
Brett, the Rays' third-round pick in 2010, ranks second in the Midwest League with 48 steals this season. He's batting .285 with six homers and 45 RBIs in 100 games after hitting .300 with 21 steals last year at Rookie-level Princeton.
Cononie, a 6-foot-7 right-hander, was 2-4 with a 4.20 ERA in 34 relief outings for the Hot Rods. He was Tampa Bay's 24th-round pick last year out of Towson, where he set a school record with 94 strikeouts as a senior.
Woodall, a left-hander drafted in the 26th-round in 2010, previously played football at the University of Alabama and was a member of the 2009 National Championship team. With Bowling Green, the reliever went 3-4 with a 4.76 ERA in 30 outings, including one spot start. He made 19 appearances last year as a rookie with Class A Short-Season Hudson Valley.
Major League Baseball has suspended 78 players this year and 22 this month due to violations of the Minor League Drug Prevention and Treatment Program. Of the suspended player, 56 have been pitchers.