Cystic kidney diseases are a clinically and genetically heterogeneous group of disorders, representing one of the most frequent genetic conditions with a prevalence of about 1 in 1000. The most important forms include autosomal dominant polycystic kidney disease (ADPKD) caused by mutations in the PKD1 and PKD2 genes and the autosomal recessive polycystic kidney disease (ARPKD) caused by mutations in the PKHD1 gene. The proteins encoded by the involved genes are summarized as cystoproteins. On the cellular level, the majority of these cystoproteins co-localize in primary cilia, the basal body or the centrosome of renal epithelial cells. Inherited polycystic kidney diseases belong to the increasing number of reported ciliopathies which include many syndromic forms, e.g. Bardet-Biedl syndrome, Meckel syndrome and Joubert syndrome. Identifying the genetic defect can help establish the correct diagnosis, define the clinical prognosis and forms the basis for genetic counselling. In addition to establishing a clinical, ultrasonographic and morphological picture of the underlying kidney disease, the algorithm of genetic diagnosis should take the presence of further organ dysfunction or malformation as well as family history into consideration.