The PAX2 gene encodes a transcription factor expressed during development. In humans, PAX2 mutations cause the renal-coloboma syndrome, whereas homozygous mutations are lethal, causing severe organ malformation, notably in the brain and kidney. Wilms tumor (WT) of the kidney results from a failure in the mesenchymal-epithelial transition, a crucial step partly controlled by PAX2. Downstream target genes regulated by PAX2 are still undefined. We therefore hypothesized that identification and characterization of the genes regulated by PAX2 may improve our understanding of developmentally related malignancies including WT. We used nickel agarose chromatin enrichment, chromatin immunoprecipitation, and the human embryonic kidney-derived cell line HEK293 to identify regulatory elements responding to PAX2. Among others, we identified WNT5A as a gene potentially regulated by PAX2. Here, we demonstrate that WNT5A is a direct target of PAX2 in HEK293 cells, using both transactivation and electrophoretic mobility shift assays. We were unable to find any WNT5A disease-associated mutations after screening a panel of 99 WT samples. However, quantitative reverse transcription-polymerase chain reaction in human favorable-histology WT revealed that ∼66% of the cases expressed significantly less WNT5A than human fetal kidney. Moreover, the WiT9 WT cell line revealed a weak expression of the WNT5A gene. A correlation of decreased WNT5A expression with predominant blastemal histology tumors suggests a possible inhibitory role in WT pathogenesis. This study underlines the importance of PAX2 in the regulation of WNT5A. Further in vivo study is necessary to determine whether the PAX2 and WNT5A are truly involved in WT pathogenesis.