BACKGROUND Chronic diarrhea during early infancy is characterized by intestinal mucosal injury, and as a consequence, the mitochondrial system of oxidation and reduction and energy production is altered. Since dietary nucleotides have been associated with the process of intestinal mucosal repair in rats with chronic diarrhea, the aim of this study was to examine the effects of dietary nucleotides on the functioning of mucosal mitochondria. METHODS Weanling rats were fed with a semipurified synthetic diet (C) or the same diet in which carbohydrates were substituted by lactose (L), resulting in chronic diarrhea. During recovery, rats were fed with the semipurified synthetic diet (LC) or the same diet supplemented with nucleotides (LN). The activities of adenosine triphosphate synthase (ATPase), cytochrome c oxidase, citrate synthase, and malate dehydrogenase were measured in mitochondria from ileum and colon mucosa. RESULTS These enzymatic activities rose in rats with chronic diarrhea, possibly to compensate for the drastic decline in adenosine triphosphate (ATP) synthesis. Dietary nucleotide supplementation allowed normalizing of the activities of ATPase (C: 0.37 +/- 0.16 microg/min/mg protein; L: 0.68 +/- 0.25 microg/min/mg protein; LC: 0.60 +/- 0.20 microg/min/mg protein; LN: 0.42 +/- 0.22 microg/min/mg protein), citrate synthase (C: 0.12 +/- 0.05 mM/min/mg protein; L: 0.21 +/- 0.07 mM/min/mg protein; LC: 0.21 +/- 0.06 mM/min/mg protein; LN: 0.12 +/- 0.02 mM/min/mg protein), and malate dehydrogenase (C: 0.77 +/- 0.48 mM/min/mg protein; L: 3.08 +/- 0.85 mM/min/mg protein; LC: 2.11 +/- 0.44 mM/min/mg protein; LN: 1.13 +/- 0.51 mM/min/mg protein) in the ileum mitochondria of the diarrheic rats. In colonic mucosa, mitochondrial enzymatic activities were restored after eliminating lactose from the diet. CONCLUSIONS These results suggest that dietary nucleotides promote earlier restoration of the ileal mitochondrial function after chronic diarrhea.