Wilms tumor (WT) is a triphasic malignant neoplasm comprised of variable proportions of epithelial, blastemal, and mesenchymal (stromal) elements. Cytogenetic analysis of these tumors has revealed a number of recurring abnormalities, including hyperdiploidy and structural abnormalities of chromosomes 1, 7, 11, and 16. We describe a WT in which apparently unrelated cytogenetic clones were detected at diagnosis, when the predominant histologic component was blastema, and after therapy, when the tumor was composed primarily of stroma. At diagnosis, a pseudodiploid karyotype was present, characterized by an X;14 insertion with concurrent deletion of 14q. In contrast, the post-therapy specimen had a hyperdiploid karyotype with a constellation of gains typical for WT. The presence of clonal abnormalities in both the blastemal and mesenchymal components of a WT supports the hypothesis that the stromal component is neoplastic, rather than reactive. The clonal abnormalities seen in different histologic components of the same WT are typically related or identical. The finding in this case of apparently unrelated clones is unusual. Possible etiologies for this biclonality, and clinical implications, are discussed.