Objectives There is a lack of data on salivary sex hormones across the menstrual cycle (MC) or hormonal contraceptive (HC) cycle of elite athletes. We aimed to provide original data on salivary sex hormones (17β-estradiol, progesterone and free testosterone) in naturally menstruating female athletes with a regular cycle or irregular cycle and using combined HC. A secondary purpose was to compare these data with published data from the general population according to the menstrual status (MC or HC or irregularly menstruating). Methods 367 saliva tests were performed on 44 elite athletes during 6 months of follow-up to certify for cycle regularity. Athletes were grouped into regular MC, n=13; irregular MC, n=5; and HC, n=26. We compared salivary data of regular MC across six cycle phases (menses, mid-follicular, late follicular, early luteal, mid-luteal and late luteal phases) with published data from women with a similar MC or HC status from the general population. Results We provided salivary original data according to six sub-phases among elite athletes with regular MC. HC athletes showed lower salivary sex hormonal levels, markedly after the first week of active HC compared with regular MC. Athletes with irregular cycles do not show a progesterone rise from the first half to the second half of the cycle (Δirregular=0.38 (1.90), a rise detectable within regular MC group ΔregularMC=2.86 (2.88)). Conclusions We provided original data for salivary sex hormone levels in elite female athletes. These references may be valuable for research investigating MC or combined HC data, particularly in longitudinal follow-ups requiring repeated measurements.