Cystic kidney diseases are clinically and genetically heterogeneous. The most important entities are autosomal-dominant and autosomal-recessive polycystic kidney diseases. The proteins encoded by the involved genes are referred to as cystoproteins, which are located predominantly in the primary cilia. Primary cilia play an important role in cyst formation. Inherited polycystic kidney diseases belong to the increasing number of reported ciliopathies, including several syndromic entities. An exact diagnosis is the basis for medical care and genetic counselling; thus, the diagnostic algorithm should include clinical, ultrasonographic and morphological features of the underlying kidney disease, knowledge about further features and family history. Molecular genetic testing may contribute important information towards a definite diagnosis.