This study aims at answering two basic questions regarding the mechanisms with which hormones modulate functional cerebral asymmetries. Which steroids or gonadotropins fluctuating during the menstrual cycle affect perceptual asymmetries? Can these effects be demonstrated in a cross-sectional (follicular and midluteal cycle phases analyzed) and a longitudinal design, in which the continuous hormone and asymmetry fluctuations were measured over a time course of 6 weeks? To answer these questions, 12 spontaneously cycling right-handed women participated in an experiment in which their levels of progesterone, estradiol, testosterone, LH, and FSH were assessed every 3 days by blood-sample based radioimmunoassays (RIAs). At the same points in time their asymmetries were analyzed with visual half-field (VHF) techniques using a lexical decision, a figure recognition, and a face discrimination task. Both cross-sectional and longitudinal analyzes showed that an increase of progesterone is related to a reduction in asymmetries in a figure recognition task by increasing the performance of the left-hemisphere which is less specialized for this task. Cross-sectionally, estradiol was shown to have significant relationships to the accuracy and the response speed of both hemispheres. However, since these effects were in the same direction, asymmetry was not affected. This was not the case in the longitudinal design, where estradiol affected the asymmetry in the lexical decision and the figural comparison task. Overall, these data show that hormonal fluctuations within the menstrual cycle have important impacts on functional cerebral asymmetries. The effect of progesterone was highly reliable and could be shown in both analysis schemes. By contrast, estradiol mainly, but not exclusively, affected both hemispheres in the same direction.