Early identification of problems with psychosocial stress regulation is important for supporting mental and physical health. However, we currently lack knowledge about when reliable individual differences in stress-responsive physiology emerge and which aspects of maternal behavior determine the unfolding of infants' stress responses. Knowledge of these processes is further limited by analytic approaches that do not account for multiple levels of within- and between-family effects. In a low-risk sample (n = 100 dyads), we observed infant cortisol and mother/infant behavior during regular play and stress sessions longitudinally from age 1 to 3, and used a three-level model to separately examine variability in infant cortisol trajectories within sessions, across years, and across infants. Stable individual differences in hypothalamus-pituitary-adrenal axis regulation were observed in the first 3 years of life. Infants of less sensitive and more intrusive mothers manifested stress sensitization, that is, elevated cortisol levels during and following stress exposure, a profile related to behavioral distress. These findings have important practical implications, suggesting that children at risk for long-term stress dysregulation may be identified in the earliest years of life.