In Sweden, shared physical custody following a parental separation has emerged as means for children to keep close relationships with both parents. Previous studies show that children benefit from regular contact with both parents, who share responsibility for their social, emotional and economic welfare. In this study, we investigate any associations between family arrangements, that is, two-parent, single and shared physical custody families and child health outcomes and whether this association was modified by parent-child communication. Data on 11- to 15-year-old children from the 2005/2006 and 2009/2010 Swedish Health Behaviour in School-aged Children survey were analysed using multivariate logistic regression. Children in shared physical custody were more likely than children in two-parent families to report multiple health complaints (OR 1.26) and low well-being (OR 1.71). When variables of parent-child communication were entered in the model, the initial differences remained between children living in shared physical custody and those living in two-parent families. Children in shared physical custody and single-parent families are more at risk of negative outcomes compared with children in two-parent families. This association was not modified by parent-child communication in children in shared custody families, indicating that the communication equals that in two-parent family children.