The Matrix was opened by Marty Balin in 1965 as a place for his new band to play. On opening night the band finally chose their name, Jefferson Airplane, and from that moment on, The Matrix was the place for the famous bands of the 1960’s in San Francisco, bridging folk and psychedelic rock. Everyone played there: The Grateful Dead, Big Brother and the Holding Company (with singer Janis Joplin), Quicksilver Messenger Service, Sopwith Camel, Country Joe and the Fish, Steve Miller Band (and later Boz Scaggs solo), Steppenwolf (then called Sparrow), The Doors (who produced a 4 album set from their 5 appearances in March 1967), The Chambers Brothers, Electric Flag, Santana, It’s A Beautiful Day, New Riders of the Purple Sage and Bruce Springsteen (in his San Francisco debut with Steel Mill).

Shows were promoted by weekly handbills that sparked an era of rock art made famous by artists such as Victor Moscoso. An entire collection titled The Neon Rose Series was inspired by the bands who played at the Matrix.

The Matrix closed in 1972 and reopened as MatrixFillmore in 2001.