Background: The Wellbeing in Special Education Questionnaire was developed to assess subjective wellbeing in young persons with intellectual and developmental disabilities (ID/DD) as this perspective is rarely included in research. The present study explored how ID/DD and gender are related to self-reported wellbeing among adolescents. Method: Students with (n = 110) or without (n = 110) ID/DD, aged 12-16 years, completed the Wellbeing in Special Education Questionnaire. Analyses of the effects of gender and disability status on peer relations and conflict, mental health, mental ill-health, school environment and family relations were carried out. Results: The experiences of the school environment and of positive mental health aspects did not differ between students with and without ID/DD, but those with ID/DD reported more mental health problems and less positive experiences of peer relations and family. Generally, boys reported more positive experiences of school and less mental health problems than girls. Conclusions: Including the subjective perspective of young persons with ID/DD through self-reports can provide essential information about wellbeing that cannot be gained from proxy ratings. The results suggest both differences and similarities in self-reported wellbeing between boys and girls with and without ID/DD and potentially also in how they perceived the concepts measured.