Trisomy 7 and 17 with deletion of Y is typical of papillary renal cell adenoma (PRCA), and additional alterations occur in the putative genetic progression toward papillary renal cell carcinoma (PRCC). Our study correlated aneuploidy with clinicopathologic features in PRCCs. We used fluorescence in situ hybridization to assess copy number for chromosomes 7, 8, 10, 12, 16, 17, and Y in 16 PRCCs and surrounding benign tubular parenchyma from 15 patients by use of alpha satellite (centromere) probes on deparaffinized tissue sections. We then compared the pattern of monosomy/nullisomy or trisomy/polysomy/hemidisomy to clinicopathologic parameters. Nine tumors (58% Group 1) showed the numeric aberrations typical of PRCAs and PRCCs, with gains of 7 and 17 and loss of Y. We also identified four trisomies of 12 and 16 and one of 8 in Group 1. The remaining seven cases (Group 2) were cytogenetically atypical. Two displayed borderline loss of chromosome 7, although trisomy 17 was present in both. Five had trisomy 7, but none exhibited chromosome 17 alterations, and two exhibited a gain of Y. Neoplasms in Group 2 were less often multicentric than were Group 1 tumors, and they contained foamy macrophage infiltrates less often. One chromophilic carcinoma with abundant clear cells and another with oncocytic features exhibited Group 2 chromosomal profiles. One patient (nuclear grade 4) died from disease, and 14 had no evidence of carcinoma at the last follow-up. We concluded that PRCCs represent a histologically and genotypically heterogeneous group of tumors. If PRCAs consistently exhibit +7, +17, and -Y, it is uncertain whether PRCCs always evolve directly from such lesions. The presence of genotypic heterogeneity might reflect histologic variants of PRCCs, which overlap with other types of RCC. PRCC is generally an indolent neoplasm, despite a high frequency of chromosomal aneuploidy.