The clinical characteristics of fistula-in-ano in infants are different from those of older children, and its treatment remains controversial. We suggest that fistula-in-ano in infants has a congenital etiology. To verify this hypothesis and to settle the controversies regarding fistula-in ano in infants, a retrospective analysis of 29 patients less than 2 years of age with anal fistulae treated between 1994 and 2009 at Samsung Changwon Hospital were reviewed retrospectively. Twenty two patients were male and mean age at diagnosis was 7.2±5.2 months. Eleven out of 22 cases had previous surgical drainage for perianal abscess. 18 patients had fistulotomy (81.8%) and four had fistulectomy (18.2%). Cryptotomies with fistulectomy were performed in 10 patients (45.5%) who had involved crypt. There was one recurrence. These results suggest that fistula-in-ano in young children less than two years of age is different from those in older children or adults. Fistulotomy is suggested to be the recommended treatment of choice. A future study involving non-operative management would be required to explore all treatment options.