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This study measured serum markers of iron status in naturally menstruating and oral contraceptive (OC) athletes during the main hormonal milieus of these two profiles to identify potential differences confounding the diagnosis of iron deficiency in female athletes. Resting blood samples were collected from 36 naturally menstruating athletes during the early‐follicular phase (EFP), mid‐ late‐follicular phase (MLFP) and mid‐luteal phase (MLP) of the menstrual cycle. Simultaneously, blood samples were collected from 24 OC athletes during the withdrawal and active‐pill phase of the OC cycle. Serum iron, ferritin, transferrin, transferrin saturation (TSAT), C‐reactive protein (CRP), interleukin‐6 and sex hormones were analyzed. Naturally menstruating athletes showed lower levels of TSAT, iron and transferrin than OC athletes when comparing the bleeding phase of both profiles ( p &lt;0.05) as well as when comparing all analyzed phases of the menstrual cycle to the active pill phase of the OC cycle ( p &lt;0.05). Interestingly, only lower transferrin was found during MLFP and MLP compared to the withdrawal phase of the OC cycle ( p &gt;0.05), with all other iron markers showing no differences ( p &gt;0.05). Intracycle variations were also found within both types of cycle, presenting reduced TSAT and iron during menstrual bleeding phases ( p &lt;0.05). In conclusion, in OC athletes, serum iron availability, but not serum ferritin, seems higher than in naturally menstruating ones. However, such differences are lost when comparing the MLFP and MLP of the menstrual cycle with the withdrawal phase of the OC cycle. This should be considered in the assessment of iron status in female athletes.   HighlightsNaturally menstruating athletes present lower TSAT, iron and transferrin in all analyzed phases of the menstrual cycle compared to OC athletes during their active pill phase. However, both the mid‐late follicular and mid‐luteal phases of the menstrual cycle do not differ from the withdrawal phase of the oral contraceptive cycle.  Intracycle variations are found for TSAT and iron in both naturally menstruating and oral contraceptive athletes, which are mainly driven by a reduction in TSAT and iron during menstrual bleeding phases.  As serum iron availability changes significantly as a function of the athlete's hormonal status, it should be considered in the assessment of the athlete's iron status as well as standardise the phase of the menstrual cycle in which to assess iron markers to avoid misdiagnosis or misleading results.  In contrast, the assessment of iron stores through serum ferritin is substantially stable and the athlete's hormonal status does not seem to be of relevance for this purpose.

Serum iron availability, but not iron stores, is lower in naturally menstruating than in oral contraceptive athletes