Eric Boucher was born in Boulder, Colorado, the son of Virginia (nee Parker), a librarian, and Stanley Wayne Boucher, a psychiatric social worker and poet. He had a sister, Julie J. Boucher, the Associate Director of the Library Research Service at the Colorado State Library (who died in a mountain-climbing accident on October 12, 1996). As a child, Eric developed an interest in international politics that was encouraged by his parents. An avid news watcher, one of his earliest memories was of the John F. Kennedy assassination.

In April 1986, police officers raided his house in response to complaints by the Parents Music Resource Center (PMRC). In June 1986, L.A. deputy city attorney Michael Guarino, working under City Attorney James Hahn, brought Biafra to trial in Los Angeles for distributing "harmful material to minors" in the Dead Kennedys album Frankenchrist. However, the dispute was about neither the music nor the lyrics from the album, but rather the print of the H. R. Giger poster Landscape XX (Penis Landscape) included with the album. Biafra believes the trial was politically motivated; it was often reported that the PMRC took Biafra to court as a cost-effective way of sending a message out to other musicians with content considered offensive in their music.  Music author Reebee Garofalo argued that Biafra and Alternative Tentacles may have been targeted because the label was a "small, self-managed and self-supported company that could ill afford a protracted legal battle." Facing the possible sentence of a year in jail and a $2,000 fine, Biafra, Dirk Dirksen, and Suzanne Stefanac founded the No More Censorship Defense Fund, a benefit featuring several punk rock bands, to help pay for his legal fees, which neither he nor his record label could afford. The jury deadlocked 5 to 7 in favor of acquittal, prompting a mistrial; despite a motion to re-try the case, the judge ordered all charges dropped. The Dead Kennedys disbanded during the trial, in December 1986, due to the mounting legal costs; in the wake of their disbandment, Biafra made a career of his spoken word performances.  Biafra has a cameo role in the 1988 film Tapeheads. He plays an FBI agent who arrests the two protagonists (played by Tim Robbins and John Cusack). While arresting them his character asks "Remember what we did to Jello Biafra?" lampooning the obscenity prosecution.  On March 25, 2005, Biafra appeared on the U.S. radio program This American Life, "Episode 285: Know Your Enemy", which featured a phone call between Jello Biafra and Michael Guarino, the prosecutor in the Frankenchrist trial.

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