Many rumors surround Thunders’ death at the St. Peter House in New Orleans, La., in April 1991. He apparently died of drug-related causes, but it has been speculated that it was the result of foul play. According to the autobiography “Lobotomy: Surviving The Ramones,” Dee Dee Ramone took a call in New York the [day after Thunders’ death] from Stevie Klasson, Johnny's rhythm guitar player. “They told me that Johnny had gotten mixed up with some bastards... who ripped him off for his methadone supply. They had given him LSD and then murdered him. He had gotten a pretty large supply of methadone in England, so he could travel and stay away from those creeps - the drug dealers, Thunders imitators, and losers like that.”

What is known for certain is that Johnny's room (No. 37) was ransacked and most of his possessions were missing (passport, makeup, clothes). Rigor mortis had set in with his body positioned in an unnatural state, described by eyewitnesses as “like a pretzel,” underneath a coffee table. Friends and acquaintances acknowledge he had not been using heroin for some time, relying on his methadone prescriptions. The police did not open a criminal investigation.

An autopsy was conducted by the New Orleans coroner, but served only to compound the mysteries. According to Thunders’ biographer, Nina Antonia, as posted on the Jungle Records Web site , the level of drugs found in his system was not fatal. And according to the book “Rock Bottom: Dark Moments in Music Babylon” by Pamela Des Barres, who interviewed Thunders’ sister Marion, the autopsy confirmed evidence of advanced leukemia, which would explain the decline in Thunders’ appearance in the final year of his life. This also sheds light on the interview in Lech Kowalski’s documentary “Born To Lose: The Last Rock and Roll Movie,” where Thunders’ sister Mary-Ann’s husband says, “Only Johnny knew how sick he really was.”

In a 1994 Melody Maker interview, Thunders’ manager Mick Webster described the efforts of his family: “We keep asking the New Orleans police to re-investigate, but they haven’t been particularly friendly. They seemed to think that this was just another junkie who had wandered into town and died. They simply weren’t interested.”