The anogenital distance (AGD) is sexually dimorphic in Mus musculus domesticus, with the male AGD approximately twice as long as that in female mice. Among female mice, the AGD varies as a function of prenatal androgen exposure. The anogenital distance index (AGDI) has been developed to serve as an indicator of prior androgen exposure due to intrauterine position (IUP). Concerns have been raised that the AGDI may not be an appropriate indicator of female IUP in mice. To further refine the AGDI, we have applied some commonly used and suggested transformations to the original data set of female CD-1 mice of known IUP, weaning body mass, and AGD. Our analysis suggests that the residual log transformation and untransformed body mass AGDIs are the most accurate means to predict the IUP of the pup. However, the IUP is only one mechanism by which a fetus may be exposed to hormonal variations in utero. Additional analyses revealed that the AGDI is influenced not only by the IUP of the female fetus but also by the identity of the dam (indicative of maternal influences) and the number of male fetuses found in the particular uterine horn. Therefore, the AGDI is not strictly a predictor of female IUP but of the intrauterine androgen environment in mice.