The non-invasive measurement of cortisol in saliva has enabled behavioral scientists to explore the correlates and concomitants of the interaction between the activity of the hypothalamic-pituitary-adrenal (HPA) axis, intrinsic factors, and social forces as they occur naturally in everyday life. The widespread integration of salivary cortisol into behavioral science has also revealed that omnipresent features of everyday life such as, over-the-counter and prescription medications, have the capacity to influence measurement validity. We identify several pathways by which pharmacologic agents could influence salivary cortisol, including (a) direct agonistic and antagonistic effects on the HPA axis, (b) indirect effects on physiological systems networked with the HPA axis, (c) moderation or mediation effects on cortisol secretion via pharmacologically induced change in subjective experience, (d) iatrogenic effects on the availability or composition of saliva, or the diffusion of serum constituents into oral fluid, and (e) cross-reactivities with antibodies used to detect cortisol by immunoassay. Specific medications with the capacity to influence salivary cortisol via these pathways are documented in an effort to procedurally and statistically minimize this potential source of error variance in the next generation of studies.