Comparative genomic hybridization (CGH) is a newly described molecular cytogenetic assay that produces a global map of DNA sequence copy number as a function of chromosomal location throughout the genome. This technique has the ability to detect discrete regions of tumor cell chromosomal imbalance (either loss or gain) which are often near loci of cellular oncogenes or tumor suppressor genes implicated in tumor development. We used CGH to detect and compare recurring cytogenetic abnormalities in both sporadic and familial cases of Wilms tumor, a common pediatric neoplasm of renal origin whose conventional cytogenetic features are complex and often difficult to interpret. For the analyses of sporadic cases, DNA was extracted from tumors of favorable histology obtained from patients of similar clinical stage; patients were divided into two groups (treatment failures and non-failures) based upon their clinical outcome. CGH demonstrated chromosome 16q deletions in patients who failed therapy, a cytogenetic feature also appreciated by allelotype analysis. In addition, previously unrecognized amplification of chromosome 1q23 as well as frequent alterations of chromosomes 6, 7, 11, 12, and 13 were also found. While familial tumors shared some of the same cytogenetic abnormalities as sporadic tumors (including deletions of chromosomes 11q and 16q as well as whole chromosome 12 gains), this group of cases was specifically characterized by a high frequency of loss on chromosomes 4q and 9p. Simultaneous 99% confidence intervals based on a mixed model provided statistical confirmation of the observed tumor-specific chromosomal imbalances. These data indicate that sporadic and familial Wilms tumors have distinct genetic abnormalities as revealed by CGH. Further, our studies refine the location of specific loci that may harbor genes of biologic importance for the development or progression of Wilms tumor.