Edited by John M. Denu Defects in the Fanconi anemia (FA) DNA damage-response pathway result in genomic instability, developmental defects, hematopoietic failure, cancer predisposition, and metabolic disorders. The endogenous sources of damage contributing to FA phenotypes and the links between FA and metabolic disease remain poorly understood. Here, using mice lacking the Fancd2 gene, encoding a central FA pathway component, we investigated whether the FA pathway protects against metabolic challenges. Fancd2 ؊/؊ and wildtype (WT) mice were fed a standard diet (SD), a diet enriched in fat, cholesterol, and cholic acid (Paigen diet), or a diet enriched in lipid alone (high-fat diet (HFD)). Fancd2 ؊/؊ mice developed hepatobiliary disease and exhibited decreased survival when fed a Paigen diet but not a HFD. Male Paigen diet-fed mice lacking Fancd2 had significant biliary hyperplasia, increased serum bile acid concentration, and increased hepatic pathology. In contrast, female mice were similarly impacted by Paigen diet feeding regardless of Fancd2 status. Upon Paigen diet challenge, male Fancd2 ؊/؊ mice had altered expression of genes encoding hepatic bile acid transporters and cholesterol and fatty acid metabolism proteins, including Scp2/x, Abcg5/8, Abca1, Ldlr, Srebf1, and Scd-1. Untargeted lipidomic profiling in liver tissue revealed 132 lipid species, including sphingolipids, glycerophospholipids, and glycerolipids, that differed significantly in abundance depending on Fancd2 status in male mice. We conclude that the FA pathway has sex-specific impacts on hepatic lipid and bile acid metabolism, findings that expand the known functions of the FA pathway and may provide mechanistic insight into the metabolic disease predisposition in individuals with FA. Fanconi anemia (FA) 2 is a human genetic disorder characterized by developmental defects, sterility, hematopoietic failure, cancer predisposition, and metabolic disease. FA is caused by biallelic mutation of any of the 22 genes encoding components of the FA pathway. Canonically, the FA pathway responds to replicative stress, particularly to DNA interstrand cross-links. FA-deficient cells are hypersensitive to genotoxins, such as DNA cross-linking agents, irradiation, alkylating agents, and oxidative stress. Endocrine and metabolic abnormalities are also components of the FA phenotype (1-3). Close to 80% of FA patients have at least one endocrine abnormality (2). Dyslipidemia has been reported in 55% of FA patients (3) and impaired glucose tolerance in 27-68% of FA patients (2-5). The endogenous agents contributing to DNA damage and the etiologic connection between FA deficiency and the development of metabolic disease remain incompletely characterized. FA phenotypes may be the direct result of DNA damage arising from endogenous sources normally counteracted by the FA pathway's DNA repair functions. This is thought to be the mechanism underlying the hypersensitivity of FA-deficient cells to aldehydes and formaldehyde by-products generated as a result of cellular ...