Objective The hypothesis that earlier menarche is associated with higher non alcoholic fatty liver disease (NAFLD) and ectopic adiposity, independent of young adult body mass index (BMI), was tested. Methods The data from 1,214 black and white women in the Coronary Artery Risk Development in Young Adults (CARDIA) study who reliably reported menarche age at exam years 0 and 2, who had multiple-slice abdominal computed tomography (CT) at exam year 25, and who had no known liver disease or secondary causes of steatosis were included. Women were aged 18-30 at year 0 and 43-55 at year 25. Liver attenuation, visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), and inter-muscular adipose tissue (IMAT) were derived from CT. NAFLD was defined as liver attenuation less than 51 Hounsfield units. Results One-year earlier menarche was associated with higher NAFLD (RR = 1.15; 95% CI: 1.07, 1.24), and VAT (6.7 cc; 95% CI: 4.3, 9.0 cc), IMAT (1.0 cc; 95% CI: 0.6, 1.4 cc), and SAT (19.6 cc; 95% CI: 13.2, 26.0 cc) after confounder adjustment. Associations remained significant (P < 0.05) after further adjustment for year 0 BMI. Only VAT remained significant (P = 0.047) after adjustment for weight gain between years 0 and 25. Conclusions Earlier menarche is positively associated with NAFLD and ectopic fat independent of confounders and young adult BMI. Weight gain between young adulthood and midlife explains some of this association.