Wilms tumor (WT) is characterized by a nonrandom pattern of chromosome aberrations, but the clinical significance of different cytogenetic patterns is unknown. The present study describes the cytogenetic findings and the clinical course in a cohort of 39 children with WT. Samples for short-term culturing and cytogenetic analysis were obtained during a 15-year period. Clonal chromosome aberrations were detected in 23 samples from 19 patients. Tumors that relapsed more often showed clonal aberrations than did tumors that did not. However, this association my have been due to sampling bias. Among the cases with karyotypically abnormal samples, the modal chromosome number was in the near-diploid range in 10, hyperdiploid/hypotriploid in 8, and hypodiploid in 1. The most common changes were trisomy 12 and gain of 1q material (8 cases each), trisomy/tetrasomy 8 (7 cases), and trisomy 13 (5 cases). None of these frequently occurring abnormalities, or the ploidy level, showed any association with clinical outcome, using tumor relapse as an end-point. Nor could any relationship between cytogenetic features and histopathologic subtype be discerned. Although the number of informative cases was too small for proper evaluation, the present study did not contradict the previous notion that loss of material from the long arm of chromosome 16 is associated with poor clinical outcome. All three patients with deletion of 16q developed metastases.