Plasma branched chain amino acid (BCAA) concentrations correlate positively with body mass index (BMI), measures of insulin resistance (IR) and severity of non-alcoholic fatty liver disease (NAFLD). Moreover, plasma BCAA concentrations also differ between the sexes, which display different susceptibilities to cardio-metabolic diseases.Assess whether plasma BCAA concentrations associate with NAFLD severity independently of BMI, IR and sex.Patients visiting the obesity clinic of the Antwerp University Hospital were consecutively recruited from 2006 to 2014.A cross-sectional study cohort of 112 obese patients (59 women and 53 men) was divided into four groups according to NAFLD severity. Groups were matched for sex, age, BMI, HOMA-IR and HbA1c.Fasting plasma BCAA concentrations were measured by tandem mass spectrometry using the aTRAQ™ method.In the study cohort, a modest positive correlation was observed between plasma BCAA concentrations and NAFLD severity, as well as a strong effect of sex on plasma BCAA levels. Subgroup analysis by sex revealed that while plasma BCAA concentrations increased with severity of NAFLD in women, they tended to decrease in men. Additionally, only women displayed significantly increased plasma BCAAs with increasing fibrosis.Plasma BCAA concentrations display sex-dimorphic changes with increasing severity of NAFLD, independently of BMI, IR and age. Additionally, plasma BCAA are associated with significant fibrosis in women, but not in men. These results highlight the importance of a careful consideration of sex as a major confounding factor in cross-sectional studies of NAFLD.