Mitochondrial dysfunction might contribute to such conditions as obesity and diabetes [1]. H55N polymorphism in the A/J strain is associated with reduced activity of mitochondrial citrate synthase (CS) [2]. The aim of the study was to investigate if mitochondrial respiration differs between the C57BL/6J (B6) strain and congenic B6.A-(rs3676616-D10Utsw1)/KjnB6 (B6.A) strain. B6.A strain carries the A/J allele in the genomic region containing the Cs gene on otherwise B6 strain background. All procedures were approved by the Lithuanian State Food and Veterinary Service for the study of 12-14 week old B6 (n=10) and B6.A (n=10) male mice fed standard chow diet. Following euthanasia, liver and hind limb muscles were excised and mitochondria were isolated by differential centrifugation [3]. The protein concentration was determined by the burette method using BSA as a standard [4]. Mitochondrial respiration was measured as oxygen consumption (O2 nM min-1 mg-1 protein) at 37°C in 1.5 ml glass vessel equipped with Clark-type oxygen electrode by using polarography system [4]. The following substrates were used: 1) 5 mM glutamate plus 5 mM malate (G+M); 2) 5 mM pyruvate plus 5 mM malate (P+M); 3) 0.25 mM malate plus 0.005 mM palmitoyl-carnitine (M+PC); 4) 5 mM glutamate plus 5 mM malate plus 0.005 mM palmitoyl-carnitine (GM+PC); 5) 5 mM pyruvate plus 5 mM malate + 0.005 mM palmitoyl-carnitine (PM+PC); 6) 5 mM succinate plus 0.001 mM rotenone (Suc+Ro). Student’s t-test was used to evaluate differences between the strains in ADP stimulated mitochondrial respiration (mt O2). Results are presented as mean±S.D.For mitochondria from the liver, mt O2 was higher in B6 compared to B6.A strain under P+M condition (33.52±10.45 vs 25.11±6.18 min-1 mg-1 protein, respectively, p < 0.05). For muscle mitochondria, the B6 strain showed higher mt O2 than B6.A strain under M+PC condition (59.51±12.81 versus 40.37±15.45, p < 0.05). In conclusion, the activity of citrate synthase may affect mitochondria metabolism in the liver and skeletal muscle.