Hernandez is facing one murder charge and five other gun-related charges. The judge ordered Hernandez held without bail pending further proceedings.
Shortly after news of his arrest, the Patriots announced that they released Hernandez.
"A young man was murdered last week and we extend our sympathies to the family and friends who mourn his loss. Words cannot express the disappointment we feel knowing that one of our players was arrested as a result of this investigation," the team said in a statement. "At this time, we believe this transaction is simply the right thing to do."
Semi-pro football player Odin Lloyd, 27, was found dead in an industrial park. His death was ruled a homicide. Family members said Lloyd was dating the sister of Hernandez's girlfriend and the two men were friends who were together at some point the night that Lloyd died. There is also evidence that the two men were together at several nightclubs over the weekend, law enforcement told ABC News.
In court, prosecutors described a killing borne out of a dispute at a Boston nightclub on the night of June 14, but they didn't say exactly what Lloyd supposedly did to anger Hernandez.
Sources told ABC News that the security system at Hernandez's home had been intentionally destroyed, and his cellphone was handed over to police "in pieces." Police also questioned why why house cleaners were hired to scrub Hernandez's mansion, sources said. Police have searched in and around Hernandez's sprawling home in North Attleborough.
Lloyd's mother, Ursula Ward, declined to comment at her Boston home Wednesday morning.
"Nothing to say, please. Thank you," she said, before shutting the door.
ABC News and The Associated Press contributed to this report.