The present study was designed to determine the relationship between body mass index (BMI) and age at menarche in girls (aged 10-19 years) living in Lima (150 m) and in Cerro de Pasco (4340 m above sea level). The purpose of the study was to determine whether the relationships between BMI and both age at menarche and chronological age differ between girls living at low and at high altitude. The ratio weight/height (the Benn index) was used in the present study as a variant of BMI because the exponent minimizes the relationship with height and maximizes the relationship with weight. From 10 to 16 years of age the Benn index of highlander girls was lower than that for girls at sea level, but at 17-19 years the differences disappeared. A later age at menarche was observed at high altitude than at sea level after controlling for socioeconomic status and for the Benn index. The value of the Benn index at the time of menarche, after controlling for chronological age in the analysis, was significantly higher at high altitude than at sea level. It was also observed that the higher the chronological age, the lower the value of the Benn index at the time of menarche. Using the median ages at menarche in Lima and in Cerro de Pasco, we found that a higher Benn index at the time of menarche is still observed at high altitude compared with girls from sea level. In Lima body weight and height were directly related to age at menarche (p < 0.001 and p < 0.005, respectively), whereas in Cerro de Pasco only weight was related to age at menarche (p < 0.001). The value of body weight at the time of menarche, after controlling for height in the analysis, was significantly higher at high altitude than at sea level. The stepwise multiple regression analysis of data from 93 girls having menarche at the time of or at most one month before the study showed that weight and altitude x height are predictors of age at menarche. These data suggest that age at menarche has an effect on both age and the Benn index acting independently and that later age at menarche in girls from Cerro de Pasco is an independent effect of altitude. Because the Benn index for menarche was different at sea level and at high altitude, we conclude that regression equations to predict age at menarche must include altitude as an independent variable.