Introduction: Urological anomalies are frequently seen in patients with anorectal malformations (ARM) and can result in upper urinary tract deterioration. Whether the current method of screening is valid, adequate and needed for all patients is not clear. We, therefore, evaluated the urological screening methods in our ARM patients for changes in urological treatment, outcome and follow-up. Methods: The medical records of 331 children born with an ARM in the period 1983-2003 were retrospectively studied. Documentation of diagnosis, screening method, urological anomalies, treatment, complications, follow-up and outcome were measured. Results: The overall incidence of urological anomalies was 52%. The incidence of urological anomalies and urological follow-up time decreased with diminishing complexity of the ARM. Hydronephrosis, vesico-urethral reflux, lower urinary tract dysfunction and urinary incontinence were encountered most. Treatment invasiveness increased with the increase of complexity of an ARM. Lower urinary tract dysfunction needing urological care occurred in 43% in combination with lumbosacral or spinal cord anomalies and in 8% with no abnormalities in the lumbosacral-/spinal region. Conclusions: Urological anomalies in patients with complex ARM are more severe than in patients with less complex ARM. Ultrasonography of the urinary tract should be performed in all patients. Voiding cysto-urethrography can be reserved for patients with dilated upper urinary tracts, urinary tract infections or lumbosacral and spinal abnormalities. All patients with complex ARM need urodynamic investigations. When using these indications, the screening for urological anomalies in ARM patients can be optimized with long-term follow-up in selected patients.