Observed seroincidence and prevalence rates in male to female (MTF) transgender individuals highlight the need for effective targeted HIV prevention strategies for this community. In order to develop an effective vaccine that can be used by transgender women, researchers must understand and address existing structural issues that present barriers to this group’s participation in HIV vaccine clinical trials. Overcoming barriers to participation is important for ensuring HIV vaccine acceptability and efficacy for the MTF transgender community. To explore barriers and facilitators to MTF transgender participation in preventive HIV vaccine clinical trials, the HIV Vaccine Trials Network (HVTN) conducted focus groups among transgender women in four urban areas (Atlanta, Boston, Philadelphia and San Francisco). Barriers and facilitators to engagement of transgender women in preventive HIV vaccine clinical trials led to the following recommendations: (1) transgender cultural competency training; (2) creating trans-friendly environments; (3) true partnerships with local trans-friendly organizations and health care providers; (4) protocols that focus on transgender specific issues; and (5) data collection and tracking of transgender individuals. These results have implications for the conduct of HIV vaccine trials, as well as engagement of transgender women in research programs in general.