BACKGROUND: It has been suggested that children with same-sex attracted parents score well in psychosocial aspects of their health, however questions remain about the impact of stigma on these children. Research to date has focused on lesbian parents and has been limited by small sample sizes. This study aims to describe the physical, mental and social wellbeing of Australian children with same-sex attracted parents, and the impact that stigma has on them. METHODS: A cross-sectional survey, the Australian Study of Child Health in Same-Sex Families, was distributed in 2012 to a convenience sample of 390 parents from Australia who self-identified as same-sex attracted and had children aged 0-17 years. Parent-reported, multidimensional measures of child health and wellbeing and the relationship to perceived stigma were measured. RESULTS: 315 parents completed the survey (completion rate = 81%) representing 500 children. 80% of children had a female index parent while 18% had a male index parent. Children in same-sex parent families had higher scores on measures of general behavior, general health and family cohesion compared to population normative data (β = 2.93, 95% CI = 0.35 to 5.52, P = .03; β = 5.60, 95% CI = 2.69 to 8.52, P = <.001; and β = 6.01, 95% CI = 2.84 to 9.17, P = <.001 respectively). There were no significant differences between the two groups for all other scale scores. Physical activity, mental health, and family cohesion were all negatively associated with increased stigma (β = -3.03, 95% CI = -5.86 to -0.21, P = .04; β = -10.45, 95% CI = -18.48 to -2.42, P = .01; and β = -9.82, 95% CI = -17.86 to -1.78, P = .02 respectively) and the presence of emotional symptoms was positively associated with increased stigma (β =0.94, 95% CI = 0.08 to 1.81, P = .03). CONCLUSIONS: Australian children with same-sex attracted parents score higher than population samples on a number of parent-reported measures of child health. Perceived stigma is negatively associated with mental health. Through improved awareness of stigma these findings play an important role in health policy, improving child health outcomes.