Non-alcoholic fatty liver disease (NAFLD) is an increasingly reported pathology, characterized by fat accumulation within the hepatocyte. Growing evidences suggest specific effects on mitochondrial metabolism, but it is still unclear the relationship between fatty liver progression and mitochondrial function. In the present work we have investigated the impact of fatty liver on mitochondrial bioenergetic functions and susceptibility to mitochondrial permeability transition (MPT) induction in animals fed a choline-deficient diet (CDD) for 4, 8, 12 or 16 weeks. Mitochondria isolated from CDD animals always exhibited higher state 4 respiration. Mitochondrial membrane potential was decreased in CDD animals at 4 and 16 weeks. At 12 weeks, oxidative phosphorylation was more efficient in CDD animals, suggesting a possible early response trying to revert the deleterious effect of increased triglyceride storage in the liver. However, mitochondrial dysfunction was evident in CDD animals at 16 weeks as indicated by decreased RCR and ADP/O, with a corresponding decrease in respiratory chain enzymes activities. Such loss of respiratory efficiency was associated with accumulation of protein oxidation products, in tissue and mitochondrial fraction. Additionally, although no differences in ATPase activity, the lag phase was increased in mitochondria from CDD animals at 16 weeks, associated with decreased content of the adenine nucleotide translocator. Increased susceptibility to calcium-induced MPT was evident in CDD animals at all time points. These results suggest a dynamic mechanism for the development of NALFD associated with altered mitochondrial function.