The first step in the degradation of branched-chain amino acids (BCAA) is transamination catalyzed by the branched-chain aminotransferase (BCAT), which is located in extrahepatic tissues. Studies of the effect of dietary protein on BCAT activity have given contradictory results. Therefore, we established the levels of BCAT activity and mitochondrial BCAT (BCATm) mRNA expression in different organs and tissues of rats. We then determined the effect of different levels of dietary protein in well-nourished rats, the effect of feeding a 0.5% casein diet for 5 wk (protein-malnourished rats) and nutritional rehabilitation of these rats with different levels of dietary protein on BCAT activity and BCATm mRNA expression in selected tissues. Finally, the response of tissue BCAT activity and BCATm mRNA levels in rats fed a 10% casein diet and injected with glucagon (4 d) or hydrocortisone (7 d) was determined. The highest concentration of BCATm mRNA was found in stomach, followed by kidney, heart, muscle, brain, skin and lung. Low levels were found in intestine, and no BCATm mRNA was detectable in liver. Although BCAT activity was significantly higher in muscle, kidney and brain from rats adapted to consume a 50% casein diet for 7 h/d for 10 d than in rats fed 6, 18 or 35% casein diets, only muscle had significantly higher levels of BCATm mRNA. In protein-malnourished rats, BCAT activity and BCATm mRNA expression in kidney, muscle and heart were not different from those of rats with free access to an 18% casein diet. Nutritional rehabilitation of the protein-malnourished rats with 50% casein for 21 d significantly increased the BCAT activity and BCATm mRNA expression in muscle. Neither hydrocortisone nor glucagon injection affected BCAT activity or BCATm mRNA concentrations in rat kidney, muscle or heart. We conclude that the nutritional regulation of BCATm is extrahepatic, tissue specific and may involve transcriptional and post-translational mechanisms.