You can make a saxophone into an electric organ; you can do everything with it.

However while Mulligan was in prison Baker transformed his lyrical trumpet style gentle tenor voice and matinee-idol looks into independent stardom. Mulligan resumed work with small groups in 1962 and appeared with other groups sporadically (notably in festival situations). In 1991 the Concordia Orchestra premiered Momo's Clock a work for orchestra (without saxophone solo) that was inspired by a book by German author Michael Ende.

Mulligan reportedly had a relationship with actress Judy Holliday until Gerry Mulligan died in 1965 and with actress Sandy Dennis from 1965 through 1973. In 1974 Mulligan met his future wife Countess Franca Rota Borghini Baldovinetti in Milan Italy. Mulligan's pianoless quartet of the early 1950s with trumpeter Chet Baker is still regarded as one of the more important cool jazz groups.