Introduction Bacterial vaginosis (BV) is the most common cause of non-specific vaginal discharge syndrome (VDS) in South African women. BV has been implicated in the acquisition of STIs and HIV. We sought to determine STI co-infection rates and associated factors in women presenting with BV-associated VDS to primary healthcare facilities (PHCs) in South Africa.

Methods Consenting adult women, presenting with VDS to PHCs in five South African provinces, were recruited in 2015–2016. Vaginal swabs were assessed for BV using Nugent scoring; and endocervical swab-extracted DNA was tested by multiplex real-time PCR for Neisseria gonorrhoeae (GC), Chlamydia trachomatis (CT), Trichomonas vaginalis (TV) and Mycoplasma genitalium. Serum specimens were tested for HIV. Data were analysed using Stata version14 using descriptive statistics and binomial regression.

Results From 717 women enrolled, 403 (56.2%) had BV. Of the 403 women with BV (median age 26[IQR 22–32], 201 [52.1%] HIV positive), 215 (53.4%) were co-infected with non-ulcerative STIs, the most common being CT [96 (23.8%)] followed by GC [86 (21.3%)].Univariable analysis for factors associated with STI co-infection showed a significant association with HIV infection, and a protective effect for condom use at last sex and attending a rural facility. In a multivariable model adjusting for the age, condom use at last sex, previous STI syndrome, HIV positivity and residence only age <35 years [relative risk (RR) 1.40 (95% CI 1.04–1.90)] and HIV infection [RR 1.27 (95% CI 1.06–1.52)] were independently associated with STI co-infection.

Conclusion A significant proportion of BV infected women had STI co-infections and associated risk factors. This has implications for syndromic management of VDS, and suggests that the strategy of stratification into STI and non-STI treatment groups should be reviewed.