Developed countries have shown a time trend towards a younger age at menarche (AAM), which is associated with increased risk of later obesity and non-communicable diseases. This study aimed to assess whether a time trend in AAM is associated with disease risk in Mexican women (n = 30,826), using data from the Mexican National Health Survey (2000). Linear and log binomial regression was used for nutritional and disease outcomes, while Welch⁻ANOVA was used to test for a time trend. AAM (in years) decreased over time (p < 0.001), with a maximal difference of 0.99 years between the 1920s (13.6 years) and 1980s (12.6 years ). AAM was negatively associated with weight (β = -1.01 kg; 95% CI -1.006, -1.004) and body mass index (BMI) (β = -1.01 kg/m²; -1.007, -1.006), and positively with height (β = 0.18 cm; 0.112, 0.231). AAM was associated with diabetes (RR = 0.95; 0.93, 0.98) and hypercholesterolemia (RR = 0.93; 0.90, 0.95), but not with hypertension, breast cancer or arthritis. In Mexico, AAM decreased significantly during the 20th century. AAM was inversely associated with adult weight and BMI, and positively with height. Women with a later AAM had a lower risk of diabetes and hypercholesterolemia.