In 1980, at the age of 15, Graffin and a few high school classmates formed Bad Religion in Southern California's San Fernando Valley.

[2] After making a name for themselves in the Los Angeles punk scene, releasing two EPs and two full-length albums, they disbanded around 1985.

However, Bad Religion reformed in 1986 with a new line-up, consisting of Graffin on vocals, Brett Gurewitz and Greg Hetson on guitars, Jay Bentley on bass, and Pete Finestone on drums.

In 1988, they released Suffer, which was a comeback for Bad Religion as well as a watershed for the Southern California punk sound popularized by guitarist Gurewitz's Epitaph Records.

After a stint with major label Atlantic Records ended in the early 2000s, Bad Religion re-signed with Epitaph and Gurewitz rejoined.

In a September 2015 interview, Graffin revealed that he had been working on his third solo album, on which he planned to continue the folk style of Cold as the Clay.

[7] After years of being out-of-print, the title of his dissertation changed to "Evolution and Religion: Questioning the Beliefs of the World's Eminent Evolutionists".

[9] In a June 2008 interview with Bad Religion bassist Jay Bentley, he mentioned that Graffin would be teaching there from January to March 2009.

[11] In 2011 the new type species Qiliania graffini of an extinct bird from the lower Cretaceous was named after Graffin "for his contributions to evolutionary biology, his public out-reach through music, and his inspiration to young scientists around the world".

[13][14] Throughout 2003, Graffin was engaged in an ongoing email discussion with Preston Jones, a historian at the Christian John Brown University in Arkansas and fan of Bad Religion.

The informal philosophical debate that resulted was published as a book titled Is Belief in God Good, Bad or Irrelevant?