The prevalence of renal stones in renal cystic and malformative conditions exceeds the prevalence of renal stones in the general population, suggesting that the above-mentioned cystic and malformative disorders favor stone formation. Urinary stasis is generally assumed to play a major part in the pathogenesis of the nephrolithiasis associated with distorted renal anatomy due to a delayed washout of crystals and risk of urinary infections. However metabolic factors are also important in the pathogenesis of stones in these conditions. Indeed, metabolic abnormalities have been observed in the majority of stone-forming patients with conditions such as horseshoe kidney and ureteropelvic junction obstruction. Five different models of stone formation can be identified, depending on stone composition, risk of infection stones, and pathogenesis of renal cystic and malformative conditions. A proper metabolic evaluation should be conducted to diagnose specific, treatable metabolic disorders, thereby reducing the frequency of recurrent stone disease in these conditions as well.