Anorectal malformations (ARM) represent a broad spectrum of patients with different level of the rectum and type of a fistula. Standardized approaches are usually successful, but patients occasionally present with an unusual course of fistula which requires a modified surgical strategy. We present here three male ARM patients with an atypical fistula which did not have connection with the urinary tract, but ran near the fistula. Case 1 has a low-type ARM with a rectoscrotal fistula running deep and partly involved in the corpus spongiosum. Anorectoplasty was performed through an anterior sagittal incision and the anterior wall of the fistula was laid open leaving the posterior wall undetached. Case 2 was diagnosed with an intermediate-type ARM with a long rectoscrotal fistula running near and parallel the urethra. Posterior sagittal anorectoplasty (PSARP) was performed leaving the fistula untouched. Case 3 presented with an intermediate-type ARM with a rectoperineal fistula adherent to the urethra. The patient was treated by PSARP leaving the fistula and part of the muscle coat of the rectum in situ. All the cases were smoothly discharged and no urological complication nor problem associated with the residual fistula was observed at the latest follow-up (17 months–2 years). Preoperative distal colostography with the aid of diverting colostomy was importantly useful for deciding surgical procedure.