General anesthesia is usually used, but on occasions local anesthesia may be used. GA affords better examination of the anus and palpation of the pilonidal cyst and is less painful. The prone jackknife or occasionally the lateral decubitus position can be used, depending on the surgeon’s preference. The prone jackknife position offers a better view of the natal cleft for the operating surgeon, and any bleeding usually runs away from the operating surgeon. Anesthetists sometimes object to the prone jackknife position, because of the physiological effects on the circulatory system and respiratory system.

The aim of the procedure is to examine the natal cleft, pilonidal sinus(es), and pilonidal abscess, then excise the pilonidal sinuses and cyst using an elliptical excision, and then pack the cavity with antiseptic gauze, alginate, or occasionally vacuum-assisted dressings. Complete removal of the sinus tracts is the main objective. The other option is marsupialization of the skin edges to the base of the wound.

The natal cleft is a narrow moist region, often containing hair, which can develop cutaneous sinuses extending deep into the subcutaneous fat almost to the deep posterior sacral fascia. Hair (usually from the head) enters the sweat glands and forms cystic collections of keratin, sebum, and hair. Multiple sinuses are common, usually close to the midline. Induration and inflammation may distort the anatomy. The pilonidal cyst may be midline or eccentric.