Renal tubular atrophy characterizes chronic progressive renal disease, but the molecular mechanisms of renal tubular cell (RTC) deletion are unclear. Because glomerular sclerosis leads to impaired peritubular blood flow, we tested the hypothesis that chronic hypoxia contributes to RTC apoptosis. Tubule hypoxia in mice with progressive renal disease (Os/+) was assessed by injecting EF5, a nitroimidazole compound that preferentially binds to cells undergoing anaerobic metabolism. Hypoxic tubules, as determined by direct immunofluorescence with anti-EF5 antibodies, were identified in kidneys from Os/+ mice, but not in age-matched controls (+/+) at 12 weeks, coincident with the onset of glomerular pathology. Hypoxia can cause apoptosis, but apoptotic RTCs were rare and equivalent in number in 12 week Os/+ and+/+ kidneys. However, by 16 weeks apoptotic RTCs were significantly more frequent in Os/+ versus+/+ mice, demonstrating that tubule hypoxia preceded RTC apoptosis. Importantly, apoptotic RTCs co-localized to hypoxic, but not normoxic tubules, indicating that tubular atrophy may result from hypoxic stimulation of RTC apoptosis. We have previously demonstrated enhanced, diffuse expression of the Fas apoptosis receptor in Os/+ tubules, providing a potential intermediary between hypoxia and apoptosis. To determine whether hypoxia stimulates Fas-dependent apoptosis, RTCs were cultured within a hypoxia chamber or in the presence of the cyanide analog, sodium azide. Both in vitro hypoxic conditions stimulated RTC plasma membrane Fas expression, and caused RTC apoptosis upon ligation with agonistic Fas antibodies. The data suggest that in the context of progressive renal disease, chronic hypoxia stimulates Fas-dependent RTC apoptosis, which represents the first definitive link between hypoxia and tubular atrophy. We believe that hypoxic induction of RTC apoptosis provides a unifying mechanism for the pathogenesis of tubular atrophy, and this paradigm identifies novel targets for chronic renal failure therapy.