Moving to New York City in 1974, Jay Dee Daugherty co-founded the Mumps with high school friends Lance Loud and Kristian Hoffman. He began playing with Patti Smith in 1975 after a brief stint as her sound man. During a hiatus while Smith healed from a serious injury from a fall off a stage, he helped rock journalist Lester Bangs form a band that included guitarist Robert Quine. He produced Bang's 7" vinyl debut, and the debut single by New York City no wave band Mars.
Since Patti Smith's re-emergence in 1995, Daugherty has continued to perform with her as a musician, co-writer, and co-producer. With Lenny Kaye and Tony Shanahan, he forms the house band for the annual Tibet House benefit concerts at Carnegie Hall.