Prevalence of co-infecting sexually transmitted infections (STIs) among patients newly diagnosed with anogenital warts is under-reported. Our objective is to determine the prevalence of six common STIs, Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), Mycoplasma genitalium (MG), genital herpes (herpes simplex virus type 2 [HSV-2]), HIV, and syphilis for patients visiting a sexual health clinic in Guangzhou, China. Demographics, sexual health, and medical histories were collected at patient intake. Patients diagnosed with anogenital warts (N = 200) were invited to participate. We collected urine samples, and urethral, cervical, and rectal swabs to test for CT, NG, and MG, and blood samples for serological detection of HSV-2, syphilis, and HIV. Overall 49 (24.5%) had a co-infection (22.2% of men and 27.7% of women). All six STIs were observed among men: CT (6.8%), NG (3.4%), MG (5.1%), HIV (4.3%), HSV-2 (4.3%), and syphilis (1.7%). Women had fewer STIs, but at higher rates: CT (13.3%), MG (6.0%), and HSV-2 (8.4%). Individual men had up to two co-infections, while women had no more than one co-infection. Chlamydia was the most common STI. Patients aged 18–25 years (35.4%) had the highest prevalence. Although opportunistic screening is often applied for high-risk groups, expansion to patients with anogenital warts in all health-care settings would improve detection of problematic asymptomatic co-infections, thereby increasing China’s capacity to contribute toward global surveillance systems.