Background: Genderqueer and nonbinary () people have remained largely invisible in health research. Previous research shows worse outcomes on health indicators for trans people when compared with cisgender controls, but the differences between binary trans and GQNB individuals are inconclusive. Aims: To compare overall health and well-being of GQNB people with controls of trans men and trans women, taking into account the impact of the additive effect of their socio-economic position, as well as their current need for gender affirming medical interventions. Methods: A community-driven survey was conducted in 2016 in five countries (Georgia, Poland, Serbia, Spain, and Sweden). Self-reported health and general well-being were analysed for differences between binary trans and GQNB respondents. The effects of multiple control variables (age, economic situation, educational level, belonging to an ethnic, religious, sexual or ability minority group, sex assigned at birth) as well as the current need for gender affirming medical interventions were controlled for. Results: The sample consisted of 853 respondents aged 16 and older, with 254 trans women (29.8%), 369 trans men (43.2%), and 230 GQNB people (26%). GQNB respondents showed significantly worse self-reported health and worse general well-being in comparison to binary trans respondents. Additional negative impacts of having a lower educational level, having more economic stress, and belonging to a disability minority group were found. Being in need of gender affirming medical interventions contributed significantly to worse self-reported health, whereas being younger contributed to worse general well-being. Discussion: In understanding health disparities between binary trans and GQNB people, it is necessary to take into account the additive effect of multiple socio-economic positions, and the current need for gender affirming medical interventions. The high proportion of GQNB respondents who report worse health outcomes highlights the need for policy makers and health-care providers in creating nonbinary-inclusive environments.