Autosomal dominant polycystic kidney disease (ADPKD) represents the most prevalent inherited kidney disease, and an important contributor to renal and systemic morbidity. Almost 20 years after the discovery of the Pkd-1 and Pkd-2 genes, the exact molecular mechanisms of polycystic kidney disease pathogenesis still remain elusive. In the absence of a specific therapy for polycystic kidney disease, patients are treated for chronic kidney disease symptoms, like hypertension, anemia, hyperparathyroidism and pain. Intensive research on ADPKD and a variety of related complex cystic kidney disease syndromes revealed a network of intracellular signaling pathways that depend on ciliary function and include calcium- and cAMP-dependent mechanisms. Furthermore, proliferative and tissue patterning responses to mTOR, STAT, CDK and wnt signaling play an important role in various aspects of cystogenesis and represent further targets for therapy. Only a limited amount of clinical evidence from randomized controlled trials is currently available to evaluate treatment options. This includes ongoing trials of the vasopressin receptor-2 antagonist tolvaptan, as well as a set of studies that fail to show a clear therapeutic benefit of everolimus or sirolimus in PKD progression. Future research will involve the evaluation of small molecule inhibitors of growth factor receptor-, CDK- and STAT-pathways, as well as the characterization of novel biomarkers of disease progression and therapeutic response.