Abstract Background The nuclear receptor corepressor 1 (NCOR1) plays an important role in the regulation of gene expression in immunometabolic conditions by connecting chromatin-modifying enzymes, coregulators and transcription factors. NCOR1 has been shown to be involved in cardiometabolic diseases. Since NCOR1 transrepresses the function of several nuclear receptors involved in hepatic lipid transport and synthesis, we hypothesized that genetic NCOR1 deletion in the liver alters lipid metabolism and atherosclerosis development. Methods To test this hypothesis, we generated hepatocyte-specific Ncor1 knockout mice on a Ldlr-/- background. Besides assessing the progression of the disease in thoraco-abdominal aortae en face, we analyzed hepatic cholesterol and bile acid metabolism at expression and functional level. Results This study findings demonstrated that specific Ncor1 knockout mice on an atherosclerosis-prone background develop less atherosclerotic lesions than controls. Interestingly, under chow diet plasma cholesterol levels of liver-specific Ncor1 knockout mice were slightly higher compared to control, but strongly reduced compared to control mice after feeding them an atherogenic diet for 12 weeks. Moreover, hepatic cholesterol and triglyceride contents were decreased in liver-specific Ncor1 knockout compared to control mice. Our mechanistic data revealed that NCOR1 reprograms the synthesis of bile acids towards the alternative pathway, which in turn reduce bile hydrophobicity and enhances fecal cholesterol excretion. Conclusions Our data suggest that hepatic Ncor1 deletion in mice decreases atherosclerosis development by reprograming bile acid metabolism and enhancing fecal cholesterol excretion. Hepatocyte NCOR1 may therefore provide a novel target for development of anti-atherosclerotic drugs.