It has been argued that the directionality of links between family functioning and substance use among adolescents is problematic to determine because adolescent substance use may influence, as well as be influenced by, interactions between parent and child (Ennett et al., 2008). Mindful that reciprocal links are plausible, such that substance use by adolescents may negatively affect parent-child interactions while poor parent-child relations can engender the increased use of cigarettes and alcohol, the present study used autoregressive, cross-lagged models to examine the interplay between these behaviours across a twelve-month period. A primary aim was to investigate whether longitudinal associations between the quality of parent-child relations and girls’ and boys’ cigarette and alcohol use would vary as a function of pubertal timing. While previous research has identified early maturation and parent-child relationship quality as risk factors for adolescent substance use, it is not clear how domains of family functioning might interact with the timing of pubertal development to influence use of cigarettes and alcohol.