The retrospective cohort study comprised 97 Balkan endemic nephropathy (BEN) and BEN-suspected patients discovered in 1971 in the field examination in the village of Šopić, one of the regions most frequently affected by the disease. Our aim was to determine the outcome of the disease in patients and to compare the survival of BEN-suspected and BEN-manifested patients and the survival of their kidneys. The mean survival time was 16.4 years for all patients (95% CI 14.51–18.21) and 23.1 years for suspected and 13.3 years for manifested patients (log-rank = 19.46; d.f. = 1; p < 0.001). According to our results, it can be concluded that BEN is characterized by slow course and prolonged evolution and that the prognosis was consistently better for BEN-suspected than for BEN-manifested patients.