It was analyzed the treatment results of 24 patients under the age of 2 years with total aganglionosis for the period from 2000 to 2013. Each of these patients underwent several surgical interventions (on the average 7.8±2.1). All children were operated radically. It was performed ileojejunorectal anastomosis at transitional fold of peritoneum in patients with concomitant short bowel syndrome. Soave's operation was done in 14 patients including by using of laparoscopic technique in 3 cases. Inflammatory complications (paraproctitis) developed in 2 children on maceration background. Perirectal fistula was observed in 1 patient subsequently. In long-term period liquid stool incontinence persisted up to 6 months in 28% of children. In terms of more than 1 year stool incontinence was observed in 12.6% of patients. Increased growth of D-lactate-producing gram-positive anaerobes was revealed during microbiological investigation of feces in 35% of patients in long-term period. Increased growth was accompanied by systemic acidosis and infectious enteritis clinically. Course monthly treatment with antibacterial drugs (Alpha-Normix, Trichopolum, Gentamicin) was prescribed in patients with short bowel syndrome and high frequent of enteritis recurrence. Treatment was used In terms from 6 to 12 months of longer if it was necessary. It was concluded that timely diagnosis and right tactic in neonatal period leads to decrease significantly the number of complications, vain interventions and to improve treatment outcomes. Our experience shows that the best results of surgical treatment were observed in children aged from 2.5-3 years when a child can control urination and defecation. The most mistakes are caused by wrong or failed morphological investigation of large bowel.