BackgroundSpecialised sexually transmitted infection (STI) clinics in the Netherlands provide STI care for high-risk groups, including female sex workers (FSW), at the clinic and by outreach visiting commercial sex workplaces with a permit. The objective was to investigate the STI positivity rate and determinants of an STI diagnosis among FSW tested by STI clinics in the Netherlands.MethodsSexually transmitted infection clinics report demographic, behavioural and diagnostic information of every consultation to the National Institute for Public Health and the Environment. We analysed all consultations of FSW between 2006 and 2013. Trends in STI positivity rate (chlamydia, gonorrhoea, infectious syphilis, HIV and hepatitis B) were analysed using χ2 for trend and logistic regression was used to analyse determinants associated with an STI diagnosis. Differences between consultations at the STI clinic and consultations during outreach were analysed using χ2 tests.ResultsThe positivity rate for any STI (overall 9.5 %) was stable from 2006 to 2013. Chlamydia positivity rate (overall 7.1 %) decreased (p < 0.001) and gonorrhoea positivity rate (overall 2.6 %) increased (p < 0.001). For gonorrhoea, the highest positivity rate was found oropharyngeal (2.0 %). Characteristics associated with STI were a younger age [adjusted odds ratio (aOR) 0.96, 95 % confidence interval (CI) 0.95–0.97 per year], a previous STI diagnosis (aOR 1.63, 95 % CI 1.38–1.92) and being notified for an STI by partner notification (aOR 2.61, 95 % CI 2.0–3.40). The STI positivity rate was significantly lower among FSW tested at outreach locations (8.6 %) compared to FSW tested at the STI clinic (11.7 %, p < 0.001).ConclusionsThe STI positivity rate among FSW remained stable, but underlying this was a decreasing chlamydia trend and an increasing gonorrhoea trend, suggesting a shift in STI risks among FSW over time. Condom use during oral sex should be promoted since oropharyngeal gonorrhoea was frequently diagnosed and because of the potential spread of antimicrobial resistant gonococci.Electronic supplementary materialThe online version of this article (doi:10.1186/s12982-015-0034-7) contains supplementary material, which is available to authorized users.