Biometric registration may improve services associated with HIV research. A cross-sectional, observational survey was used to evaluate biometric fingerprint scanning for identification (ID) verification in the setting of an HIV prevention study. Survey outcomes were dichotomized (discouraged or not discouraged) by biometric scanning and statistical analyses were used to determine if participation decreased by greater than 10% overall and after stratifying by demographic variables and risk behaviors. 206 participants were recruited from a community-based HIV and sexual health research screening program. Participants completed a quantitative survey to assess their perceptions of biometric scanning for ID verification. The majority of participants (n = 160; 77.7%) indicated no deterrence from testing due to biometric scanning, yet a significant number (n = 45; 23.3%, P < .001) reported at least partial deterrence. Research using biometric scanning for ID verification may significantly limit access to HIV prevention services and may risk reducing meaningful participation among marginalized populations.