He was denying charges that he executed his friend Odin Lloyd, 27, and possessed weapons illegally.
Hernandez said that he was not the gunman that murdered Lloyd, a semi-pro football player from Boston. Lloyd's body was found June 17 in an industrial park less than a mile from Hernandez's North Attleborough mansion.
He also mouthed "I love you" to his fiancee, Shayanna Jenkins. Jenkins' presence in the courtroom was unexpected, as prosecutors say she remains a person of interest in the case.
Lloyd will continue to be held at a Bristol County jail until a separate bail hearing is held on October 9. Hernandez has been in separated from other inmates in jail since his arrest in June.
He was formally indicted earlier this month, and his case has moved to superior court, where the murder trial will be held.
Hernandez's attorneys will use the circumstantial evidence against their client at the bail hearing in October, but Hernandez is unlikely to be released on bail as another shooting investigation with possible links to the former player is pending.
"In a sense, this is like the opening kickoff," Hernandez attorney Charles Rankin said after the arraignment, "and we have a long way to go before the trial."
"We are confident that, at the end of the trial, Aaron Hernandez will be exonerated. We encourage everyone to keep an open mind. We feel confident when evidence is presented in a court of law Aaron Hernandez will be exonerated."