OBJECTIVE Total colonic aganglionosis (TCA) is a relatively uncommon and severe condition managed by pediatric surgeons. Several procedures exist for the treatment of TCA. However, there is no current consensus on a superior operative procedure. The objective of this article is to evaluate the comparative effectiveness of the Soave procedure and the Martin procedure in the treatment of TCA with respect to preoperative data and postoperative outcome. METHODS In the period from January 2001 to June 2008, we recruited 29 patients with TCA who were treated with the Martin procedure (14) or the Soave procedure (15). Relevant data were collected from the medical charts kept in the hospital library. The follow-up study used a detailed questionnaire that was answered by patients either by telephone or directly in the clinic. In the clinic, data, including age, body weight before operation, intraoperative blood transfusion, anastomotic leakage, postoperative enterocolitis, durations of any postoperative fever, days in hospital, and a range of functional outcomes, were particularly recorded to enable a comparison of the effectiveness of the Soave procedure and the Martin procedure. RESULTS A male predominance has been described for patients with TCA, with a male-to-female ratio of approximately 6.25:1. In the Soave group, time between ileostomy and the definitive procedure, body weight before the definitive procedure, and the operative age were less than those in the Martin group (P < .05). In patients who underwent the Martin procedure, the average duration of postoperative fever and days in hospital were significantly more than those in the Soave group (P < .05). In the Soave group, the incidence of intraoperative blood transfusion (46.7%), abdominal wound infection (6.67%), and anastomotic leakage (0) was significantly less (P < .05) than those in the Martin group (92.8%, 28.5%, and 14.3%, respectively). In the follow-up study, 7 patients in the Martin group had enterocolitis, and 4 of them had severe enterocolitis leading to multiple hospitalizations. In contrast, in the Soave group, only 2 patients had enterocolitis, and 1 was ameliorated after the therapy of anus dilation in the clinic. During the 4 weeks after the operation, all patients had an increased frequency of defecation, with soiling in the perianal area. At 3 months after the operation, there were significantly more patients with normal defecation in the Martin group compared to the Soave group (P < .05). Six months later, 11 (78.6%) patients in the Martin group and 8 (61.5%) patients in the Soave group had normal defecation and the difference was still significant (P < .05). CONCLUSIONS Patients with TCA managed with the Soave procedure had fewer operative complications compared with those of patients who underwent the Martin procedure. However, the patients managed with the Soave procedure took longer to establish normal defecation. Although each procedure has advantages and disadvantages, the Soave procedure is promising for the treatment of TCA, especially with regard to postoperative complications. A long-term follow-up study is needed.