Background: The regulation of hypothalamic pituitary adrenal (HPA) axis contributes to individual differences in health and human development. The cortisol awakening response (CAR), the diurnal slope, and the area under the curve (AUGg) are some tactics used to index daily HPA axis functioning. Salivary cortisol samples were assessed from participants transitioning to college. A latent trait factor of cortisol was derived to reflect both within- and across-wave trait components of the variance in cortisol. The latent trait cortisol (LTC) was found to be distinct from the CAR. Findings document the reliability, divergent and convergent validity, and stability of a latent trait factor of individual differences in HPA axis activity that may provide a cost efficient alternative to existing strategies and minimize participant burden.