Within-family concordance in physiology may have implications for family system functioning and for individual health outcomes. Here, we examine patterns of association in cortisol within family triads. A total of 103 adolescents and their parents sampled saliva at multiple timepoints before and after a conflict discussion task. We explored whether within-family associations existed and were moderated by stepparent presence and youth gender, and whether within-family patterns of influence correlated with individuals’ aggregate cortisol. Across the laboratory visit, the cortisol levels of fathers, mothers, and youth were positively associated. In time-lagged models, mothers’ cortisol predicted fathers’ cortisol levels sampled at the following timepoint, whereas fathers’ predicted youths’ and youths’ predicted mothers’ cortisol. These patterns appeared stronger in families not including stepparents. Youth gender moderated some associations: in the aggregate, youth were more strongly linked with their same-gender parent. In time-lagged models, girls were more closely linked to their mothers than boys, and both parents were more linked to girls. Youth showed higher aggregate cortisol output if they were more linked with their mothers, and lower output if more linked with their fathers; parents had higher output if they were more linked with their spouses and lower output if more linked with their children. These results suggest that family members’ physiological activation may be linked during shared interaction, and that these patterns may be affected by family role and by youth gender. Our findings identify specific patterns of physiological influence within families that may inform family systems theories.