To assess potential barriers and facilitators to participation in bio-behavioural surveillance surveys of men who have sex with men and transgender women (trans women) in Jamaica, we recruited participants for individual interviews and focus group discussions. Respondents included 3 trans women; 46 gay, bisexual and other men who have sex with men; and 3 cis gender women. Data from 46 men and 3 trans women were analysed to describe barriers and facilitators to participation in research. Barriers identified were: lack of perceived benefits from research participation due to high socioeconomic status; concerns about confidentiality and unintended disclosure; HIV fatigue and fear of knowing one's HIV status; distrustful inter-group dynamics; and undesirable study location and hours. Facilitators to participation in research were: belonging to a marginalised subgroup of men who have sex with men or trans women; incentives; and trust in researchers and community input in planning the study. Findings emphasise the need to understand the individual, interpersonal and structural factors that shape relationships, disclosure and interactions to successfully enrol diverse samples of men who have sex with men and trans women.