Eating disorder (ED) pathology is increasingly recognized among males; however, presentations within males differ from traditional descriptions of ED pathology in females. Additionally, experiences of ED pathology differ between sexual minority (SM) and heterosexual males. These differences suggest that existing ED assessments, which are primarily based on female samples, do not adequately capture ED pathology in SM and heterosexual males. The Eating Disorder Examination-Questionnaire (EDE-Q) is a commonly used assessment of ED pathology; however, at present the factor structure of this instrument in SM and heterosexual males is unclear. This study aimed to determine the most appropriate factor structure of the EDE-Q by evaluating proposed factor structures in a large, non-clinical sample consisting of heterosexual and SM men. Additionally, this study examined differences in the factor structures and severities of ED pathology between SM and heterosexual males. Confirmatory Factor Analyses examining existing factor structures of the EDE-Q indicated that the brief three-factor model was the best fitting model for both heterosexual and SM males. Subsequent comparisons of factor scores between groups indicated that SM males in our sample experienced higher levels of dietary restraint, overvaluation of shape and weight, and body dissatisfaction than heterosexual males. Results provide preliminary support for the use of the brief three-factor model of the EDE-Q when assessing ED pathology among SM and heterosexual males in non-clinical research settings.