Background: The aim of this study was to measure young people’s health status and explore associations between health status and belonging to one or more socio-culturally marginalised group. Methods: part of the Access 3 project, this cross-sectional survey of young people aged 12–24 years living in New South Wales, Australia, oversampled young people from one or more of the following groups: Aboriginal and or Torres Strait Islander; living in rural and remote areas; homeless; refugee; and/or, sexuality and/or gender diverse. This paper reports on findings pertaining to health status, presence of chronic health conditions, psychological distress, and wellbeing measures. Results: 1416 participants completed the survey; 897 (63.3%) belonged to at least one marginalised group; 574 (40.5%) to one, 281 (19.8%) to two and 42 (3.0%) to three or four groups. Belonging to more marginalised groups was significantly associated with having more chronic health conditions (p = 0.001), a greater likelihood of high psychological distress (p = 0.001) and of illness or injury related absence from school or work (p < 0.05). Conclusions: increasing marginalisation is associated with decreasing health status. Using an intersectional lens can to be a useful way to understand disadvantage for young people belonging to multiple marginalised groups.