When athletes optimize their physical performance, an imbalance could occur between the strain of training, time for recovery and the athlete’s individual tolerance of stress that could lead to overreaching and overtraining syndrome. Cortisol has been suggested to be a biological, diagnostic marker to detect overreaching and overtraining syndrome, since it is thought to indicate stress. This study aimed to provide normative data on cortisol levels, hence investigate seasonality and impact of oral contraceptive use to elucidate if cortisol could be used as a diagnostic marker to detect overreaching and overtraining syndrome in female athletes. The women, divided in two groups, oral contraceptive users (n = 15) and non-users (n = 18), were followed over a nine-month period with monthly blood sampling for cortisol testing and a Profile of Mood State questionnaire (POMS) as a subjective measure of overreaching and overtraining syndrome.Findings indicated seasonal variations in cortisol levels, with different pattern in oral contraceptive users to non-users and moreover, higher cortisol levels in users to nonusers irrespective of season. No differences in seasonal variation in Global POMS score within the groups and no differences in Global POMS score between the groups were detected. Due to seasonality, impact of oral contraceptive use on cortisol levels, methodological considerations and standardization, as well as due to no convincing relationship to Global POMS score, cortisol is not suggested to be an optimal biological, diagnostic marker to detect overreaching and overtraining syndrome in physically active women.