Amoeba Music is a Bay Area institution and one of those places that you have to visit at least once. And if you're looking for music (or movies) you will definitely find something you like. Amoeba sells new and used stuff, in all formats (CD, tape, vinyl, VHS, DVD, etc.). If you're looking for something from your youth or a hot new band, you can get it at Amoeba. I like to peruse the bargain bins for random stuff and the occasional gem. Be prepared to invest some time in the store, but it's worth it.
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