HIV-1 infection disproportionally affects African-American and Latino men who have sex with men (MSM). Their inclusion in biomedical and behavioral research is critical to understanding and addressing HIV vulnerability. Using focus groups, we sought to understand the perceptions related to participating in biomedical research of acute/recent HIV-1 infection (AHI) using complex sampling and data collection methods to reach this hidden group at highest risk of acquiring and transmitting HIV. Given the potential impact of AHI on HIV transmission in MSM, it is important to understand this intersection for HIV prevention, care, and treatment purposes. The aim of this study was to understand how recruitment and data collection methods affect AHI research participation willingness particularly among MSM of color. Findings suggest that major barriers to research participation with complex sampling to identify AHI and intensive risk behavior collection such as diary methods are lack of anonymity, partner disclosure, and study fatigue. The authors explore implications for future study designs and development based on these findings.