Harbaugh, who turns 49 next month, reported to Stanford Hospital for what the team said was a minor procedure.
"Coach Harbaugh is not at the facility today under doctor's orders," a statement on the 49ers' website stated. "He is having a minor procedure done at Stanford Hospital today for an irregular heartbeat.
"We anticipate that he will be back at the facility [Friday] but do not have any further information to share at this time.
"Assistant head coach and special teams coordinator Brad Seely will be overseeing today's practice and meetings."
San Francisco plays the Chicago Bears at home Monday night. The 49ers lead the NFC West with a 6-2-1 record after tying St. Louis on Sunday. Chicago is an NFC North-leading 7-2.
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