Array comparative genomic hybridization was used to identify copy number alterations in clear cell renal cell carcinoma (ccRCC) patient tumors to identify associations with patient/clinical characteristics. Of 763 ccRCC patients, 412 (54%) provided frozen biopsies. Clones were analyzed for significant copy number differences, adjusting for multiple comparisons and covariates in multivariate analyses. Frequent alterations included losses on: 3p (92.2%), 14q (46.8%), 8p (38.1%), 4q (35.4%), 9p (32.3%), 9q (31.8%), 6q (30.8%), 3q (29.4%), 10q (25.7%), 13q (24.5%), 1p (23.5%) and gains on 5q (60.2%), 7q (39.6%), 7p (30.6%), 5p (26.5%), 20q (25.5%), 12q (24.8%), 12p (22.8%). Stage and grade were associated with 1p, 9p, 9q, 13q and 14q loss and 12q gain. Males had more alterations compared with females, independent of stage and grade. Significant differences in the number/types of alterations were observed by family cancer history, age at diagnosis and smoking status. Von Hippel-Lindau (VHL) gene inactivation was associated with 3p loss (P<E-05), and these cases had fewer alterations than wild-type cases. The fragile site flanking the FHIT locus (3p14.2) represented a unique breakpoint among VHL hypermethylated cases, compared with wild-type cases and those with sequence changes. This is the first study of its size to investigate copy number alterations among cases with extensive patient, clinical/risk factor information. Patients characterized by VHL wild-type gene status (vs sequence alterations) and male (vs female) cases had more copy number alterations regardless of diagnostic stage and grade, which could relate to poor prognosis.