Sex differences in fear and anxiety have been widely reported although results are not entirely consistent depending on measures used. Also, a possible influence of the menstrual cycle is often not taken into account, and effect sizes are not always discussed. In a sample of healthy young adults (n=111 women without hormonal contraceptives and n=107 men) the acoustic startle response (ASR) and emotional ASR modulation were analysed. We found no significant effect of sex on ASR (p=.269) but a significant effect of menstrual cycle (p=.027, η2=0.105). Compared to men, women showed increased ASR during the late luteal phase probably reflecting elevated negative emotionality, and during ovulation which, however, might be due to increased auditory sensitivity and changes in general CNS arousal. Neither sex nor menstrual cycle affected startle modulation. Thus, at least in young adults, menstrual cycle but not sex per se appears to contribute significantly to ASR variance.