The effect of the female genital tract on sperm is not well known. To investigate the effect of cervical mucus on the lipid content of human sperm, we co-incubated sperm and mucus samples in vitro such that the sperm were able to swim in and out of the mucus samples. High performance liquid chromatography and UV detection were used to measure the lipid contents of the sperm and cervical mucus before and after migration. The concentrations of cholesterol, vitamin E, sphingomyelin, diacyls and plasmalogens in sperm were all approximately 45% lower after migration in cervical mucus and the cervical mucus was found to be enriched in some of these lipid species after the sperm migration. These results suggest that the cervical mucus selects a subpopulation of sperm with a lower lipid content. However, a concomitant efflux of various lipid classes from the sperm to the cervical mucus cannot be ruled out.