To fully understand the potentially harmful effects of prenatal stress exposure impacts, it is necessary to quantify long-term and episodic stress exposure during pregnancy. There is a strong body of research relating psychological stress to elevated cortisol levels in biomarkers. Recently, maternal hair has been used to measure cortisol levels, and provides the unique opportunity to assess stress exposure throughout gestation. Understanding how cortisol in the hair is related to more common biomarkers, such as, blood, saliva and urine is currently lacking. Therefore, we developed a biokinetic model to quantify the relationships between hair, blood, saliva and urine cortisol concentrations using published literature values. Hair concentrations were used to retrospectively predict peaks in blood and saliva concentrations over days and months. Simulations showed realistic values in all compartments when results were compared with published literature. We also showed that the significant variability of cortisol in blood leads to a weak relationship between long-term and episodic measurements of stress. To our knowledge, this is the first integrative biokinetic cortisol model for blood, urine, hair and saliva. As such, it makes an important contribution to our understanding of cortisol as a biomarker and will be useful for future epidemiological studies.