Despite many efforts of scientists and epidemiologists, the aetiology of endemic nephropathy (EN) is still unknown. This disease occurs in the rural population of geographically limited areas of Bulgaria, Bosnia and Herzegovina, Croatia, Romania, and Serbia, and a number of theories have been proposed about its aetiology. The mycotoxin theory has prevailed until now, based on the studies of nephrotoxic mycotoxin ochratoxin A (OTA) that revealed higher frequency of OTA-positive food and blood samples in endemic than in non-endemic areas. However, a new aristolochic acid (AA) theory of EN origin has been proposed recently, due to the histological similarities in kidney lesions between patients suffering from EN and patients suffering from Chinese herbs nephropathy caused by AA. Until now it has not been unequivocally proved that the inhabitants of EN areas are exposed to higher concentration of AA than in other regions and the exposure pathways are rather uncertain. This paper presents most important studies supporting both theories, indicating also the inconsistencies of each.