Background Identifying and treating genital infections, including sexually transmitted infections (STI), among newly diagnosed human immunodeficiency virus (HIV)-infected individuals may benefit both public and individual health. We assessed prevalence of genital infections and their correlates among newly diagnosed HIV-infected individuals enrolling in HIV care services in Namibia. Methods Newly diagnosed HIV-infected adults entering HIV care at 2 health facilities in Windhoek, Namibia, were recruited from December 2012 to March 2014. Participants provided behavioral and clinical data including CD4+ T lymphocyte counts. Genital and blood specimens were tested for gonorrhea, Chlamydia, trichomoniasis, Mycoplasma genitalium, syphilis, bacterial vaginosis, and vulvovaginal candidiasis. Results Among 599 adults, 56% were women and 15% reported consistent use of condoms in the past 6 months. The most common infections were bacterial vaginosis (37.2%), trichomoniasis (34.6%) and Chlamydia (14.6%) in women and M. genitalium (11.4%) in men. Correlates for trichomoniasis included being female (adjusted relative risk, [aRR], 7.18; 95% confidence interval [CI], 4.07-12.65), higher education (aRR, 0.58; 95% CI, 0.38-0.89), and lower CD4 cell count (aRR, 1.61; 95% CI, 1.08-2.40). Being female (aRR, 2.39; 95% CI, 1.27-4.50), nonmarried (aRR, 2.30; (95% CI, 1.28-4.14), and having condomless sex (aRR, 2.72; 95% CI, 1.06-7.00) were independently associated with chlamydial infection. Across all infections, female (aRR, 2.31; 95% CI, 1.79-2.98), nonmarried participants (aRR, 1.29; 95% CI, 1.06-1.59), had higher risk to present with any STI, whereas pregnant women (aRR, 1.16, 95% CI 1.03-1.31) were at increased risk of any STI or reproductive tract infection.