BACKGROUND The aim of the study was to compare clinical outcomes and quality of life in patients undergoing surgery for pilonidal disease with unroofing and marsupialization (UM) or rhomboid excision and Limberg flap (RELP) procedures. METHODS One hundred forty consecutive patients with pilonidal sinus were randomly assigned to receive either UM or RELP procedures. A specifically designed questionnaire was administered at three months to assess time from the operation until the patient was able to walk, return to daily activities, or sit without pain, time to return to work or school, and time to healing. Postoperative pain was assessed with a visual analog scale and the McGill Pain Questionnaire. Patients' quality of life was evaluated with the Cardiff Wound Impact Schedule (CWIS). Questionnaires were administered by a clinician blinded to treatment. RESULTS Compared with RELP, patients receiving UM had significantly shorter duration of operation and hospital stay, shorter time periods to walk, return to daily activities, or sit without pain and to return to work or school, and fewer complications. Time to final healing was significantly shorter and quality of life scores on the CWIS were higher in patients receiving RELP than in those receiving UM. Patients with UM had lower levels of pain one week after surgery. CONCLUSIONS The unroofing and marsupialization procedure provides more clinical benefits in the treatment of pilonidal disease than rhomboid excision and Limberg flap and should be considered the procedure of choice. However, it may be associated with more inconvenience in wound care and longer healing time than rhomboid excision and Lindberg flap.