Intrauterine exposure to the rainy season in the tropics may be accompanied by high rates of infection and nutritional deficiencies. It is unknown whether this exposure is related to the extrauterine timing of development. Our aim was to evaluate the relations of prenatal exposure to the rainy season and altitude of residence with age at menarche. The study included 15,370 girls 10 to <18 years old who participated in Colombia’s 2010 National Nutrition Survey. Primary exposures included the number of days exposed to the rainy season during the 40 weeks preceding birth, and altitude of residence at the time of the survey. We estimated median menarcheal ages and hazard ratios with 95% confidence interval (CI) according to exposure categories using Kaplan–Meier cumulative probabilities and Cox proportional hazards models, respectively. All tests incorporated the complex survey design. Girls in the highest quintile of gestation days exposed to the rainy season had an earlier age at menarche compared with those in the lowest (adjusted hazard ratios (HR)=1.08; 95% CI 1.00–1.18, P-trend=0.03). Girls living at altitudes ⩾2000 m had a later age at menarche compared with those living <1000 m (adjusted HR=0.88; 95% CI 0.82–0.94, P-trend <0.001). The inverse association between gestation days during the rainy season and menarche was most apparent among girls living at altitudes ⩾2000 m (P, interaction=0.04). Gestation days exposed to the rainy season and altitude of residence were associated with the timing of sexual maturation among Colombian girls independent of socioeconomic status and ethnicity.