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I run into the City from time to time for business meetings. I ALWAYS park at one of the attended City run parking lots. I see it as an insurance policy. Prices aren't as high as other lots.
I'm not from SF, but will be visiting for a day soon. I'm concerned about the car break-ins I've been reading about. Does anyone have a recommendation for a safe place to park near the Embarcardero & Ferry Building area?