BACKGROUND: The etiology of nephrocalcinosis is variable. In this study, we wanted to elucidate whether the histopathological appearance of calcium phosphate deposits provides information about possible etiology. METHODS: Autopsy cases from the years 1988 to 2007 and native kidney biopsies from a 50-year period (1959-2008) with nephrocalcinosis were identified. The biopsy cases were re-evaluated by light microscopy. The autopsy cases were analysed according to the underlying disease. The biopsy cases were grouped with respect to the likely etiology of nephrocalcinosis. Total number, density, localization, size and pattern of all calcification foci were documented and correlated with clinical and laboratory data. RESULTS: About 223 of 12 960 autopsy cases (1.7%) had nephrocalcinosis, 111 of which (49.8%) suffered from advanced malignant tumours. Nephrocalcinosis was the main diagnosis in 48 of 12 480 native kidney biopsies (0.4%). Clinicopathological correlation revealed a specific pattern of calcification associated with hyperphosphataemia and/or hyperphosphaturia: these cases showed predominant globular or shell-like calcifications (phosphate type). In contrast, the biopsies of the hypercalcaemic/hypercalciuric group had a different predominant pattern with clumpy or finely granular calcifications (calcium type). CONCLUSIONS: Our results indicate that hyperphosphaturia-associated cases of nephrocalcinosis can be distinguished from hypercalciuria-associated cases histopathologically.