We evaluated 22 boys and 2 girls 1 month to 8 years old with imperforate anus to determine the relationship between neurogenic voiding dysfunction and bony sacral or spinal cord anomalies. Lower urinary tract function before anorectoplasty was normal in 12 children (group 1), abnormal (detrusor-sphincter dyssynergia) in 9 (group 2) and not evaluated in 3 (group 3). High lesions of imperforate anus were present in 22% of the patients in group 1 and in 100% of those in group 2. Plain radiography revealed partial sacral agenesis in 1 child in group 1 and 4 in group 2. Magnetic resonance imaging detected occult spinal dysraphism in 1 patient in group 1 and 2 in group 2. (Occult spinal dysraphism included sacral lipoma, tethered cord, syringomyelia and thick filum terminale.) Seven children in group 2 had vesicoureteral reflux before anorectoplasty. All children in group 2 were placed on clean intermittent catheterization for the management of neurogenic voiding dysfunction. Normal upper urinary tract function was maintained in all patients in group 1 and 6 in group 2. The remaining 3 children in group 2 had high grade reflux at presentation associated with severe renal damage or noncompliance with clean intermittent catheterization. These findings indicate that in children with imperforate anus lower urinary tract function should be evaluated before anorectoplasty because of the high incidence of associated congenital neurogenic voiding dysfunction and the potential risk for renal deterioration. When possible, neurogenic voiding dysfunction should be managed with clean intermittent catheterization to prevent renal damage.