Background: The mechanisms whereby rat hepatocytes undergo irreversible injury due to a lack of oxygen have not been established. Methods: Liver cells were used for reperfusion injury, and four compartmentalized pathways were evaluated during hypoxia (N-2/CO2, 19:1) for 30 min followed by oxygen (O-2/CO2, 19:1) for 30 min. Results: Cell viability decreased during the hypoxic, but not during the reoxygenation, phase. Glycogenolysis, as measured by glucose release, was significantly increased during hypoxia as compared to controls in oxygen (205 +/- 15 vs. 155 +/- 10 mmol glucose/mg protein/h, respectively), and did not return to normal levels by reoxygenation. Gluconeogenesis was importantly decreased during hypoxia (102 +/- 10 vs, 8 +/- 2 nmol glucose/mg protein/h) with partial recovery during reoxygenation, Ureagenesis diminished in hypoxia, but recovered during reoxygenation. Additionally, 3-hydroxybutyrate formation was augmented by hypoxia, with some recovery when oxygen was present. Conclusions: These results suggest that compartmentalized pathways are protected from hypoxic injury in isolated hepatocytes, and also suggest it as a model to test the idea that enzymes of those pathways are organized into multienzyme complexes in vivo.