This study compared the lipid profile of women runners with menstrual cycle irregularities with their normally menstruating counterparts. Relationships among selected steroid hormones and serum lipid levels in 10 eumenorrheic (EU) and 8 oligo-/amenorrheic (O/A) women runners and 6 eumenorrheic controls (CON) were examined. Serum 17 beta-estradiol (E2), progesterone (Prog), and dehydroepiandrosterone-sulfate (DHEAS) concentrations were determined in daily blood samples for 21 days, and integrated concentrations were calculated. Fasting blood samples were analyzed for total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), HDL2, HDL3, triglycerides (Trig), and apolipoproteins A-1, A-II, and B. The O/A group had significantly lower E2 and Prog than EU or CON groups. Women in the CON group had lower HDL-C and HDL3 than the runners. With all women grouped together, E2 was not significantly correlated with any measured blood lipid parameters. On the other hand, DHEAS was significantly correlated with HDL-C, HDL2, and apolipoprotein A-I. These data demonstrate that women runners, regardless of menstrual cycle status, exhibit higher HDL-C concentrations than CON and supports previous research reporting a positive association between DHEAS and HDL-C.