Surgical excision is an effective option for those with chronic pilonidal cysts. Often performed in an outpatient setting, the procedure consists of a surgeon removing all affected tissue in the surrounding area. Afterward, the wound is packed with a sterile dressing and left open. Depending on the patient, it can take anywhere from a few weeks to several months to recover completely. Most individuals can return to work after two to four weeks, as long as they avoid strenuous activities.

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