Advances in molecular genetics have led to the identification of more than 70 different genes involved in the development of cystic kidney diseases. Most of these diseases are rare, and interpreting the resultant plethora of disease-causing mutations requires a methodical and meticulous approach to differential diagnosis. In this Review we discuss a clinical approach to the diagnosis of cystic kidney diseases in adults, for use by nephrologists. This approach is based upon a thorough clinical evaluation, which considers both kidney phenotype and extrarenal manifestations of the underlying disorder, in combination with genetic testing in selected patients. In our view, cystic kidney disease can (in the majority of patients) be reliably classified on the basis of clinical findings. We therefore propose that defining clinical situations to precipitate the initiation of genetic testing is mandatory and cost-effective. New techniques such as next-generation sequencing will facilitate the diagnosis of cystic kidney diseases in the future, increasing diagnostic safety in a subset of patients. In renal tumour syndromes, genetic testing is warranted.