Salivary cortisol (sCort) and salivary alpha-amylase (sAA) constitute proxy measures of the two major stress response systems, i.e. the hypothalamic-pituitary-adrenal axis and the autonomic nervous system, respectively. Potentially confounding determinants of sCort and sAA may limit a reliable concurrent measurement of both biomarkers, if not adequately considered. We reviewed the most important determinants of sCort and sAA and provide recommendations for handling these potential confounders. We focused on a selection of confounders, resulting in an in-depth consideration of age, sex steroid-related factors, somatic health, acute medication, smoking, consumption of food and drinks, alcohol consumption, physical activity/fitness, and sleep. Our review further highlights the importance of the consideration of potential confounders for a reliable and valid simultaneous measurement of sCort and sAA. We further provide recommendations about which and how to handle relevant confounders in the study design or data analysis.