Background The impact of sex differences on chronic liver disease (CLD) and hepatic encephalopathy (HE) is unknown. The majority of animals used in research are male since the main difficulty with using female animals is the potential impact of the estrous cycle, increasing intragroup variability. The bile duct ligated (BDL) rat is a well-characterized model of CLD and HE in males which has not been investigated in females. Therefore, we aimed to characterize a female BDL model of CLD and HE and compare to male BDL rats. Material and methods Female rats underwent either BDL (n=8) or Sham (n=8) surgery. After 5 weeks, we assessed estrous cycle phase (by cellular cytology), anxiety (open field test), motor incoordination (rota-rod test) and night-time activity. We also assessed body weight, body composition (MRI), gastrocnemius muscle weight/circumference, grip strength, and ammonia and liver enzymes in plasma. Results from female BDL rats were compared to historical laboratory data from male BDL rats. Results Female BDL rats had increased liver enzymes (ALP (P=0.001) and AST (P<0.0001) (but not ALT)), bilirubin (P<0.0001) and ammonia (p<0.001), and decreased albumin (P<0.0001) compared to female Shams. These results were comparable to male BDL rats except ALT and ammonia which were lower in females (p< 0.01). Female BDL rats did not differ in body weight, muscle circumference/weight and grip strength but had decreased fat mass (p<0.0001), increased lean mass (p<0.005) compared to female shams. Whereas, male BDL rats have decreased fat mass, muscle circumference/weight and grip strength. BDL in female rats induced a dysregulated estrous cycle compared to Sham (increased metestrus phase (p<0.01)). Similar to male BDL rats, female BDL rats had increased anxiety (p<0.005), motor incoordination (p<0.05), and decreased night activity (p<0.05) independent of the estrous cycle phase. Discussion We demonstrated BDL surgery in females leads to hepatic and neurological impairment comparable to male BDL rats (similar intra-group variability). Interestingly, female BDL rats developed unique features. Contrary to male BDL vs Shams, body weight and muscle mass does not differ between female BDL and Shams. Since muscle mass plays an important compensatory role in regulating ammonia levels, this could explain why the increase in blood ammonia levels in female BDL rats (vs. female Shams) was lower compared to male BDL. We expect that this model will provide new insights on the effect of sex differences on the pathogenesis of CLD and HE and help to personalize HE treatment.