Hernandez was arrested early Wednesday at his North Attleboro, Mass., home. Police did not release the cause for his arrest warrant at the time, but announced his charges in Attleboro District Court.
The Patriots cut Hernandez shortly after his arrest, before the charges were announced.
A crowd including Lloyd's family arrived in court to see Hernandez's arraignment, where Hernandez was charged with murdering Lloyd and five counts of firearm possession.
Lloyd, 27, had known Hernandez for about a year, and Lloyd's girlfriend is the sister of Hernandez's fiancee. A jogger found his body dumped in an industrial park near Hernandez's house, and police found that keys in Lloyd's pocket went to a car rented in Hernandez's name.
Police officers searched Hernandez's house three times last week and executed a warrant to retrieve surveillance footage from his security system, which has 14 cameras.
They found that the tape was missing between 6 and 8 hours of footage from around the time of the murder. Hernandez was reported to have smashed the security system and destroyed his cell phone. They were able to recover text messages sent to Lloyd by Hernandez and to two other suspects the night Lloyd was murdered.
Authorities have tape of Hernandez with a firearm, saying "You can't trust anyone anymore" shortly before driving to pick up Lloyd, the prosecutor said.
The end of the security tape shows the three men, without Lloyd, coming back to the house. One of the men was carrying a gun into the house and down to the basement. The tape was destroyed beyond that point.
A shell casing was found in Hernandez's rental car.
Hernandez did not initially submit a plea in court.