Vannatter was last seen in early October 2003. He was living with a roommate, John Caputo, in a rental home on east 345th Street in Eastlake, Ohio. Caputo said Vannatter came home with a man named Mark, whom Caputo hadn't met before, and the two men had drugs and drug paraphernalia. Mark's last name is unknown. Caputo was on probation and didn't want drugs in the house. There was a minor physical altercation between the three men, and Vannatter and Mark left the residence. Vannatter has never been heard from again.

Vannatter's family was unconcerned by his absence at first. He had dropped out of sight before for as long as a month at at time due to his drug addiction, and his relatives believed he was probably staying with friends temporarily. When Thanksgiving came and went without his loved ones hearing from him, his mother and stepfather reported him missing. His mother stated it would be uncharacteristic of him to run off with someone he'd just met.

After Vannatter's disappearance, Caputo quickly disposed of all his belongings; he later said he'd done it because he was angry at Vannatter. Police believe Caputo may know more about Vannatter's disappearance than he's disclosed, but no suspects have been named in the case. Vannatter's family describes him as a good-hearted man who loved animals and children. Foul play is suspected in his disappearance; it remains unsolved.