Development of the perineum as well as the external genitalia is determined by dihydrotestosterone, resulting in a greater anogenital distance (AGD) in males than females. In animal experiments with hormonally active agents, anogenital distance is used as a bioassay of fetal androgen action. Use of anogenital distance in human studies has been rare. Because anogenital distance has been an easy-to-measure, sensitive outcome in animal studies, we developed an anthropometric protocol for measurement of anogenital distance in human males. In this paper we describe the method for measurement of three anogenital distances, their reliability, and an assessment of predictors for each in the context of an epidemiological study. We compare the reliabilities and predictors to those for stretched penis length and penis width. A cross-sectional study of 781 newly delivered male infants was conducted in 2002-03 in Chiapas, Mexico. Replicate measures were obtained on nearly all subjects. The reliability of the measures of anogenital distance (0.82-0.91) were higher than for stretched penis length (0.78) and width (0.75). Birthweight and gestational length were more strongly related to anogenital distance than to penis length. Anogenital distance was not related to penis length (r = 0.03). Our large study clearly shows that AGD can be measured well in newborn males, and that the measurements were more reliable than those of penis length. Whether AGD measures in humans relate to clinically important outcomes, however, remains to be determined, as does its utility as a measure of androgen action in epidemiological studies.