Molecular tumor markers are used to aid the differential diagnosis of renal cell carcinoma and to monitor disease progression and recurrence. They may also provide prognostic information and help in the design of therapeutic regimens. So far, no satisfactory markers are available for the diagnosis of renal cell carcinoma. Many markers have been evaluated for their potential use as prognostic factors. Some are promising, yet need vigorous clinical trials to validate. Genetic changes detected by molecular and cytogenetic methods provide markers specific for renal cell carcinoma. High-throughput DNA and tissue microarray techniques promise to revolutionize the discovery and validation of novel molecular markers.