Sexually transmitted infections (STIs) remain a global issue, causing health problems and financial burdens. This study aimed to provide an update on the invasive pathogens and analyze any associated factors in patients visiting Da Nang Dermato-Venereology Hospital who were diagnosed with genital tract infections in males and lower genital tract infections in females; 535 participants underwent clinical examinations and microbiological tests to identify the invasive microorganisms, before we analyzed previously gathered laboratory results and associated risk factors. The rate of infection was 37.6% amongst 535 participants. Treponema pallidum infection accounted for the highest rate of 21.3%, followed by HSV, standing at 6%. The prevalence of syphilis infection was highest in the 20–29 age group, standing at 51.7%. There was a positive correlation between age under 20 and infected conditions (OR = 3.78, 95% CI: 1.41–10.11, p = 0.008). Having multiple sexual partners was identified as a risk factor for infection, as those with three or more sexual partners showed a high correlation (OR = 3.19, 95% CI: 1.44–7.05, p = 0.004). The high syphilis prevalence among young adults and teenagers underscores the need for improved STI education and screening programs in Vietnam.