Villous atrophy in an infant immediately suggests food intolerance. We report a case with an unusual cause. This female infant was first examined at 5 months for anorexia and failure to thrive. Intestinal biopsy showed total villous atrophy. A diet excluding gluten and cow milk proteins failed to improve her condition and the infant was hospitalized at 7 months for further investigations. The infant was hypotonic with a head lag. No other clinical sign was noted. Serum transaminases were increased 5- to 10-fold and CSF proteins concentration was increased. Metabolic investigations revealed hyperlactacidaemia and an increased lactate/pyruvate ratio during fasting and feeding, suggesting a mitochondrial cytopathy. Respiratory chain enzymatic activity measurements confirmed the diagnosis and showed severely decreased activities of complexes I, III and IV in both the liver and muscle. Molecular analysis demonstrated depletion of mitochondrial DNA in the liver (75%) and in muscle (97%). The infant was discharged under continuous enteral nutrition. Improvement was of short duration and the infant died at 1 year of age of massive hepatic failure. This is the first report of a mitochondrial DNA depletion with total villous atrophy and malabsorption as early clinical onset. A mitochondrial cytopathy should be considered in such conditions when food exclusion diets fail.