Emerging adult (EA) cortisol response during family interaction predicts change in EA anxious behavior during the transition to college (Johnson & Gans, in press). In the present study, we take an initial step toward integrating family systems research and physiology by including assessment of EA salivary cortisol collected during a triadic (mother–father–EA offspring) family interaction task. Emerging adults (N = 101) between the ages of 17 and 19 were assessed at 3 time points across their first college year: the summer before college, Fall and Spring semesters. Two parents accompanied the emerging adult child to the summer assessment; all family members provided 4 saliva samples each at 20-min intervals. Later assessments of emerging adults included measures of internalizing behaviors. EA’s cortisol secretion patterns during family interaction predict observed and self-reported family relatedness, as well as patterns of internalizing behavior during the college transition. Observed family functioning appeared to moderate the relationship between EA cortisol response during family interaction and anxious behavior when adapting to college. Different patterns of results emerged, however, for EA men and women. The approach taken by this study provides a first step toward understanding how interrelationships among elements of physiology and family functioning contribute to later adjustment.