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Steroid hormones are often assessed via saliva samples, as they are noninvasive and easy to collect. However, hormone levels in saliva can fluctuate from moment-to-moment, are influenced by factors such as momentary emotional states and food intake, and some vary strongly across women's ovulatory cycle. In contrast, hormone levels in hair seem to be more robust against these influences and were previously suggested to be a good alternative to obtain women's baseline hormone levels. In the current study, we investigated whether hormone levels are stable across multiple assays and whether hormone levels from saliva and hair samples correlate. We collected saliva and hair samples from N = 155 naturally cycling women across two ovulatory cycles. All samples were analyzed for progesterone, testosterone and cortisol levels via mass spectrometry (LC-MS/MS). Results showed that both averaged saliva and hair hormone levels were moderately stable across cycles. Hair progesterone levels showed higher stability than the respective levels from saliva. Saliva and hair levels for progesterone and testosterone were moderately correlated, whereas cortisol levels from saliva and hair were only weakly correlated. Results suggest that the type of sample from which baseline hormone levels are assessed and the cycle phase in which saliva samples are collected may have a high impact on the obtained results. Implications for future studies are suggested.