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 which increases intra-group 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, plasma ammonia and liver enzymes. Results from female BDL rats were compared to historical laboratory data from male BDL rats. Results Female BDL rats had increased markers of liver injury: ALP, AST and bilirubin (p<0.001) and impaired markers of liver function (increased ammonia and decreased albumin (p<0.001)) compared to female Shams. Furthermore, Female BDL rats did not differ in body weight, muscle circumference/weight and grip strength but had decreased fat mass (p<0.0001) and increased lean mass (p<0.005) compared to female shams. All results were comparable to male BDL rats except for plasma ammonia levels which were significantly lower in females (p<0.01). Moreover, male BDL rats had decreased fat mass, lean mass, muscle circumference/weight and grip strength. BDL surgery in female rats induced a dysregulated estrous cycle compared to sham (increased metestrus phase (p<0.01)). However, 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 did not differ between female BDL and Shams. Since muscle mass plays an important compensatory role in regulating ammonia levels, this could explain the reason why blood ammonia levels in female BDL rats are significantly lower compared to male BDL rats. 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.