Despite intensive research the knowledge of stone pathogenesis, which is the basis of every rational stone metaphylaxis, has remained rather scanty. Epidemiology shows that stone formation in most patients is only a sporadic event, probably resulting from a coincidence of different factors. The hypercalciuria, hypocitraturia, hyperuricosuria and hyperoxaluria frequently found in calcium stone formers can be influenced therapeutically and, in affluent societies, seem to be the result of protein over-consumption. These four factors favour crystallization processes in urine. However, urine is normally protected from nucleation, growth and aggregation of calcium minerals by crystallization inhibitors. In urine, crystallization of calcium oxalate can only be induced by an extreme supersaturation, a deficient inhibitor activity and promoters of crystallization. To form a stone, crystals have to be retained in the urinary collecting system. Two mechanisms of retention are discussed: large crystal aggregates trapped in collecting ducts of renal papillae, or a pre-existing calcification of the papilla (mainly calcium phosphate) that may be responsible for growth of an initially fixed particle to a concretion large enough to become symptomatic. An excessive oxalate intake combined with a low calcium consumption can produce marked hyperoxaluria. In the animal model, hyperoxaluria induces not only calcium oxalate crystallization but also papillary damage and incrustrations. Hypercalciuria at a low pH favours the aggregation of calcium oxalate, and at a high pH the crystallization of calcium phosphate, a promoter of heterogeneous nucleation of calcium oxalate. All these factors and further complex phenomena mentioned in this paper have to be taken in account to perform rational stone metaphylaxis.