Objective The Damus–Kaye–Stansel operation sometimes results in deteriorating semilunar valve insufficiency. We verified the semilunar valve function after the Damus–Kaye–Stansel operation and compared the end-to-side Damus–Kaye–Stansel with the double-barrel Damus–Kaye–Stansel. Methods Forty-seven patients who underwent the Damus–Kaye–Stansel operation between June 1993 and August 2008 were retrospectively reviewed. Any patient who underwent a Norwood-type operation was excluded. The median age at operation was 19 months (range, 0–276 months). Forty-five patients were Fontan candidates. Thirty-nine patients underwent pulmonary artery banding before the Damus–Kaye–Stansel operation. Twenty-two patients had undergone an arch repair previously. The semilunar valve function was evaluated by echocardiography. Results Thirteen patients underwent the end-to-side Damus–Kaye–Stansel operation, and 34 patients underwent the double-barrel Damus–Kaye–Stansel operation. The mean follow-up period was 71 ± 50 months (range, 1–188 months). Although there were 4 deaths, no death was related to the Damus–Kaye–Stansel procedure. Two of the patients with early death could not undergo a postoperative evaluation of the semilunar valves. The semilunar valve regurgitation mildly deteriorated in 7 patients (pulmonary regurgitation in 5 patients and aortic regurgitation in 2 patients). Pulmonary regurgitation deteriorated from none to mild in 1 patient, none to trivial in 2 patients, and trivial to mild in 2 patients. Both deteriorations in aortic regurgitation ranged from none to trivial. Semilunar valve regurgitation did not affect patients' circulatory condition. The end-to-side Damus–Kaye–Stansel operation more frequently caused a deterioration in pulmonary regurgitation than the double-barrel Damus–Kaye–Stansel operation (4/11 vs 1/34, P  = .001). No surgical intervention for a systemic ventricular outflow obstruction was observed in the follow-up period. Conclusions The double-barrel Damus–Kaye–Stansel operation was found to be superior to the end-to-side Damus–Kaye–Stansel operation for the prevention of postoperative pulmonary regurgitation.