Neuroendocrine dysfunction is hypothesized to be an early emerging vulnerability marker for depression. We tested whether the main and interactive effects of maternal psychopathology and early child temperamental vulnerability for depression assessed at age three predicted offspring's basal cortisol function at age 6 years. 228 (122 males) children participated in the baseline and follow-up assessments. At age three, maternal lifetime psychopathology was assessed with a diagnostic clinical interview, and child temperamental positive affectivity (PA) and negative affectivity (NA) were assessed using laboratory observations. At age six, children's waking and evening cortisol were assessed on 2 days. Maternal lifetime anxiety predicted offspring's higher morning cortisol at age six. Child temperamental NA at age three predicted higher evening cortisol at age six. There was a significant interaction between maternal lifetime depression and child temperamental PA at age three in predicting offspring's morning cortisol at age six. For the offspring of mothers with lifetime depression, higher PA at age 3 predicted lower morning cortisol at age 6. These findings highlight the importance of examining the main and interactive effects of maternal psychopathology and early child temperamental vulnerability in predicting the development of offspring's stress physiology. Findings hold significance in identifying etiological mechanisms of risk and delineating the complex developmental pathways to psychopathology.