In the 1950s and early 1960s he played with Horace Silver, Maynard Ferguson and Art Blakey and the Jazz Messengers, for whom he eventually became musical director. From 1964 to 1970 he played in the Miles Davis Quintet, for which he composed extensively ("Prince of Darkness," "ESP," "Sanctuary," etc.). In 1970 he was one of the founding members of Weather Report, and remained a member till 1985. He also recorded critically acclaimed albums as leader, notably Native Dancer and Atlantis.
Until 1968 he played tenor saxophone exclusively. By the early 1970s, however, he chiefly played soprano saxophone, perhaps because it could be heard more easily among electronic instruments.
Since leaving Weather Report he has continued to record in jazz fusion styles, as well as more bebop oriented settings.
Shorter has been quite prolific, recording dozens of albums, and appearing on dozens more with others. Many of his recordings for Blue Note Records are regarded as classics. His 2003 album Alegria received a 2004 Grammy Award for Best Instrumental Jazz Album.
His brother is trumpeter Alan Shorter.