SUMMARY Transgender (trans) individuals are those who have a gender identity that does not match their birth-assigned sex. About 1.4 million adults in the United States identified as transgender in 2016. Trans people may take gender-affirming hormones or have undergone gender-affirming genital surgery. Little is known about approaches to sexual health screening and management, as well as risk for acquisition of sexually transmitted infections or development of other genital pathologies, in this population. The NIH has thus identified a major need for innovative research addressing the medical, sociological, psychological and structural causes and consequences of transgender and gender nonconforming identities. About of trans women (people assigned male at birth but with a female gender identity) have undergone vaginoplasty (surgical creation of a neovagina, typically using penile and scrotal skin) and while symptoms, such as malodor, discharge and irritation are commonly reported, little is known about the underlying pathophysiology. The vaginal microbiome in cis women is a critical determinant of health, yet our understanding of the composition and role of microbiota colonizing the neovagina is scarce and completely lacking for immune outcomes. In trans men, vaginectomy is rare (<2%), however an estimated 69% use gender-affirming testosterone therapy. Masculinizing hormone therapy has significant effects on the vaginal epithelium that result in reduced cellular proliferation and glycogen production. This is similar to vaginal atrophy observed during menopause in cis women, which affects the vaginal microbiota and has negative impacts on sexual health and quality of life. Little information is available on the relationship between vaginal microbiota and inflammation and the development of vaginal atrophy and symptoms in trans men. Given these unknowns, the short-term goals of this research are to better understand the causes of genital symptoms and the impact of these symptoms on sexual health and quality of life in trans women and men. We will achieve these goals establishing the TransBiota study and characterizing the immunological and microbiological vaginal microenvironments in trans women and men (Aim 1) and then testing for correlations between the vaginal microenvironment and patient characteristics, including sexual behaviors and hygiene practices (vaginal exposures), and importantly vaginal symptoms (Aim 2). We will implement an innovative home-based sampling strategy and an innovative statistical strategy that affords scientific rigor by correcting for experimental errors associated with microbiome analyses. Understanding the vaginal microenvironment and its role in sexual health in trans women and men is an important prerequisite to the development of clinical best- practices, which are currently lacking. The long-term goals of this study are to improve vaginal care for trans women and men and to ultimately leverage this information for the development of novel interventions to achieve optimal vaginal health and protection.