A recently observed developmental instability of the ano-genital distance (AGD) in female mice indicates that natural prenatal androgens do not have such a robust effect on female genital morphology as has been generally assumed. Part of this instability might be caused by oestrous cyclicity. To check this assumption, we examined the effect of the stage of the oestrous cycle on the AGD in adult (61–75 days old) female mice. Consistent with our assumption, the female AGD (1) varied during the oestrous cycle (p < 0.05), indicating thus rapid changes in morphology of female external genitalia, and (2) showed good repeatability (>0.66) in each stage of the oestrous cycle, suggesting that female genital morphology systematically varied within the oestrous cycle. Therefore, the stage of the oestrous cycle should be considered when assessing prenatal masculinization in adult female mice.