The pyruvate dehydrogenase complex (PDC) plays a critical role in lipid synthesis and glucose homeostasis in the fed and fasting states. The central role of the liver in the maintenance of glucose homeostasis has been established by studying changes in key enzymes (including PDC) and the carbon-flux via several pathways under different metabolic states. In the present study we have developed a murine model of liver-specific PDC deficiency using Cre-loxP technology to investigate its consequences on lipid and carbohydrate metabolism. There was no incorporation of glucose-carbon into fatty acids by liver in vitro from liver-specific Pdha1 knockout (L-PDHKO) male mice due to absence of hepatic PDC activity. Interestingly, there was a compensatory increase in lipogenic capacity in epididymal adipose tissue from L-PDHKO mice. Both fat and lean body mass were significantly reduced in L-PDHKO mice, which might be explained by an increase in total energy expenditure compared with wild-type littermate mice. Furthermore, both liver and peripheral insulin sensitivities measured during a hyperinsulinemic-euglycemic clamp were improved in L-PDHKO mice. The findings presented here demonstrate (i) the indispensable role of PDC for lipogenesis from glucose in liver and (ii) specific adaptations in lipid and glucose metabolism in the liver and adipose tissue to compensate for loss of PDC activity in liver only.