Several studies reported a significant influence of ovarian hormone status on cognition and person perception. In particular, it has been stated that female mating preferences are shifted during the menstrual cycle. It remains, however, unclear if facial emotion recognition, a prerequisite for successful social interaction, is also influenced by estradiol and progesterone levels. Hence, we investigated 32 healthy right-handed females, 15 during their follicular phase and 17 during their luteal phase and compared their recognition accuracy. Hormone levels were correlated with several neuropsychological parameters. Subjects were matched for age and education and did not differ in any neuropsychological function. Analysis of emotion recognition performance (ANOVA) revealed a significant effect of phase, showing higher accuracy in the follicular group. Furthermore, a significant negative correlation between progesterone level and emotion recognition performance emerged, indicating higher accuracy with lower progesterone levels, hence supporting the group differences. Our results indicate a significant association of menstrual cycle phase and thus ovarian hormone concentration on facial emotion recognition, with progesterone exerting a special influence on this social-emotional ability.