Renal-cell carcinoma (RCC) is an important cause of morbidity and mortality, and its incidence has been increasing. Malignant transformation is thought to be associated with changes in the expression of several genes, and this alteration in gene expression is believed to be critical to the development of the malignant phenotype. In this study, the expression of about 60,000 genes/expressed sequence tags in clear-cell RCC, normal kidney, and a set of diseased nonmalignant kidneys was determined with the use of the Affymetrix microarray technique, and differences in gene expression were analyzed. Many genes were found to be differentially expressed in these two sample sets. The genes that were expressed greater than four times more in RCC, those expressed only in RCC, and those expressed greater than two times more in RCC and also expressed in a limited number of other tissues were analyzed for their expression in a variety of other normal and diseased tissues. Some of the genes identified were overexpressed only in RCC among the tissues examined, and some were overexpressed in several other malignant tissues in addition to RCC. Other genes were overexpressed in RCC compared with normal kidney but were also overexpressed in diseased nonmalignant kidney or a variety of other normal tissues. All of the RCC samples could be clustered together, separate from the normal and diseased kidney samples, with the use of the Eisen clustering technique and a set of 50 genes. The observed changes in gene expression in RCC should help further the understanding of the biology of RCC and may be useful in diagnosis, treatment, and imaging.