Brandon Banks and Corey Batey, each 19, and Brandon Vandenburg, 20, entered their pleas at an arraignment hearing in Nashville, 12 days after they were indicted on charges of aggravated rape and sexual battery.
A fourth indicted player, Jaborian McKenzie, 19, pleaded not guilty earlier in the case, in which prosecutors alleged the four assaulted a woman June 23 in Vandenburg's dormitory room.
The four players were dismissed from the team June 29 pending a police investigation.
Each were charged with five counts of aggravated rape and two counts of aggravated sexual battery, while Vandenburg also faces charges of tampering with evidence and unlawful photography.
Banks, Batey and McKenzie are free on bond, while Vandenburg remains in custody.
A fifth player, junior starting wide receiver Chris Boyd, has also been charged in connection with the case an accessory after the fact. Boyd, considered one of the nation's top collegiate receivers, made 50 catches for 774 yards last season.
He has been suspended from the Commodores.
2014: The Year in Music [PHOTOS]