[1] Located at 3138 Fillmore Street in Cow Hollow, in a 100-capacity beer-and-pizza shop,[1][2][3] The Matrix opened 13 August 1965, showcasing Jefferson Airplane, which singer Marty Balin had put together as the club's "house band".

[5] The Matrix was a favorite haunt of gonzo journalist Hunter S. Thompson in the late 1960s – it was mentioned briefly in Fear and Loathing in Las Vegas during a flashback scene.

In the early years of The Matrix, there was a huge mural of the Four Horsemen of the Apocalypse on the left wall near the rear; rumor was that the members of Jefferson Airplane had painted it before the club first opened.

The entrance was recessed about two feet and was left of center on the windowless wall seen from the street, and there was a cabinet outside to the door's right where upcoming bands were listed and handbills were posted.

This brought a distinct change to the booking policy whereby Jabberwock favorites Country Joe and the Fish, the New Age and Blackburn & Snow performed.

In 1968, after finally getting all the necessary releases, The Matrix's owners sold to Columbia Records some tapes of live sets from 1966 by The Great Society (the band Grace Slick belonged to before replacing Signe Anderson[10] in Jefferson Airplane).

Edits of those tapes (including the first commercial recordings of "White Rabbit" and "Somebody to Love") eventually became two LPs, Conspicuous Only in Its Absence and How It Was (promoted as by "Grace Slick & The Great Society").

As part of its contract, Columbia Records also created a custom mixing board for the club, hoping for additional tapes of future live performances.

When The Matrix closed, a nearby bar, Pierce Street Annex, leased the space and moved in, remodeling once again, and turned it into a nightclub with only a DJ and no live music.

After the Pierce Street Annex closed, then-Mayor Gavin Newsom's company, PlumpJack Group, took over in 2000 and renamed the space The MatrixFillmore.