Metanephric adenoma has morphologic similarities to papillary renal cell neoplasms. Cytogenetic studies of papillary renal cell carcinoma and papillary adenoma have shown frequent gains of chromosomes 7 and 17 and loss of the Y chromosome. Some cytogenetic studies have supported the hypothesis that metanephric adenoma is related to papillary renal cell neoplasia; others have not. Seven metanephric adenomas were studied with fluorescence in situ hybridization in paraffin sections using centromeric probes for chromosomes 7, 17, and Y diluted 1:100 with tDenHyb1 buffer. The signals in 100 to 200 nuclei were counted in each tumor. Samples of histologically normal renal cortical tubule epithelium were used as controls. In all seven metanephric adenomas, the results for chromosomes 7 and 17 were similar: a high percentage of nuclei with two signals (range, 75 to 85%; median, 79%). Normal kidney showed similar results (range, 78 to 88%; median, 84%). The Y chromosome was present in all three of the tumors from males (range, 86 to 89% of nuclei; median, 87%). Normal kidney gave similar results (range 82% to 91%, median 84%). The presence of chromosomes 7, 17, and Y in metanephric adenomas is similar to their presence in normal kidney. Metanephric adenoma lacks the frequent gains of chromosomes 7 and 17 and losses of the Y chromosome that are typical of papillary renal cell neoplasms, supporting the notion that metanephric adenoma is not related to papillary renal cell carcinoma and papillary adenoma. Genetic analysis of chromosomes 7, 17, and Y may facilitate discrimination of metanephric adenoma from papillary renal cell carcinoma in difficult cases.