Now he is saying it was catastrophic to his career.
Eric Harris and Dylan Klebold gunned down 12 students and one teacher at their Colorado high school before taking their own lives.
At the time, it was erroneously reported that the shooters were fans of Manson's music.
The singer now says "If [the Columbine killers] had just bought my records, they would be better off. Certain people blame me for the shootings at schools."
"That's going to be a great pull-quote for you," he told The Guardian. "But, honestly, the Columbine era destroyed my entire career at the time."
Manson is currently promoting his new album titled "Heaven Upside Down."
In 2012, he said the title for his "Born Villain" was influenced by having been been wrongfully vilified because of Columbine.