Hemolytic uremic syndrome (HUS) is a very rare disease (two cases per year per 1 million population) but represents the most common cause of acute renal failure in young children that require dialysis. The majority of cases in childhood (90%) is caused by Shiga toxin producing Escherichia coli infection. This typical form of the disease does not relapse and has a good prognosis if the acute status can be managed successfully. Atypical HUS (aHUS) is a severe and frequently relapsing disorder with the same triad of thrombocytopenia, hemolysis and acute renal failure in the absence of Shiga toxin E. coli infection. More than 50% of patients with atypical HUS progress to chronic renal dysfunction and 10% die due to complications of the disease. Atypical HUS appears to have a genetic basis. Mutations in genes coding for components of the alternative complement pathway are found in about 60% of cases. The clinical presentation of aHUS overlaps with that of other thrombotic microangiopathies, rendering the diagnosis on clinical grounds alone extremely difficult. In recent years, genetic testing has opened the way for molecular diagnostics and helped establishing therapeutically and prognostically useful genotype-phenotype correlations. This review summarizes recent findings regarding the genetic basis of the HUS. The pathophysiology of the disease and the implication of genetic abnormalities in the complement system for the different types of HUS are discussed.