The store on Clement Street in the inner Richmond, and the store on Gough Street in Hayes Valley are closing for good starting Monday.
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Walgreens says prescriptions are being moved to other nearby locations.
RELATED: 5 more San Francisco Walgreens to close; SF Supervisor says it's directly related to retail theft
Rampant shoplifting in San Francisco has been cited for why the stores are closing.
Earlier this year, ABC7 News reporter Lyanne Melendez shot viral video of a shoplifter clearing out shelves at the Gough Street Walgreens.
RELATED: Thief steals garbage bag full of items from SF Walgreens with security filming in plain sight
Out-in-the-open theft at SF Walgreens caught on video
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Another location on Cesar Chavez Street will close on Wednesday. Once that closes, that would be the fifth store to close this month.
In a statement to ABC7 News, Alexandra Brown from Walgreens writes:
"Due largely to ongoing organized retail theft, we have made the difficult decision to close five stores across San Francisco. Each store will transfer prescriptions to a nearby Walgreens location within a mile radius and we expect to place the stores' team members in other nearby locations.
Organized retail theft continues to be a challenge facing retailers across San Francisco, and we are not immune to that. Retail theft across our San Francisco stores has continued to increase in the past few months to five times our chain average. During this time to help combat this issue, we increased our investments in security measures in stores across the city to 46 times our chain average in an effort to provide a safe environment.
Patients will not need to take any action; their prescriptions will automatically transfer to a nearby Walgreens and they can expect to receive additional information in the mail."