The past two decades have witnessed recognition of several new types of renal cell carcinoma, each with distinct cytogenetic abnormalities. Included are several genetic and acquired cystic kidney diseases associated with development of renal cell carcinoma, the topic of this review. The risk in patients with autosomal dominant polycystic kidney disease is not accurately known but may be slightly increased. The risk for patients with von Hippel-Lindau disease is substantial, and death from renal cancer is common. For patients with tuberous sclerosis complex, the challenge is recognition of the occasional malignancy arising in a field of many benign tumors. Patients with end-stage kidney disease and acquired cystic kidney disease may develop a variety of renal cell carcinoma types. Progress in understanding the molecular basis of renal cyst formation and neoplastic disease has fostered development of targeted therapies that now hold promise for a group of neoplasms whose cure was traditionally dependent on surgical approaches.