In 2011, the qualitative study on exploring sexual identities and sexual health of men having sex with men in Iloilo City began with the use of focus group discussion as a research strategy. This research as subject of this case study was urged by the increasing sexually transmitted infections/HIV cases reported in the city of the western region of the Philippines. The focus group discussion was a viable tool for data collection as the study was guided by the health belief model commonly framed within the health education and other health researches. Using this lens, the study necessitated an in-depth, rich, and substantial quality of data drawn from lived experiences of a marginalized population considered to be most at risk of sexually transmitted infections/HIV. The study generated four focus group discussions of varying group types of sexual minority men based on sexual identities and orientation. Upon its completion, this research became the impetus of further research interests on sexual health and behaviors whereby the current statistics generated by health agencies are now paralleled with actual accounts of lived experiences of sexual minority men. This case explains the concerns and issues on recruitment/sampling, the conduct of focus group discussion in the context of sexual health and behaviors, and the practicalities learned in the use of focus group discussion. The focus group discussion as a research tool was utilized to facilitate a better understanding of a commonly described taboo issue of sexual behaviors and the gay community.