Background The objectives of study were to determine trends in syphilis prevalence, trends in the proportion screened and to compare with unscreened for syphilis amongst pregnant women attending 15 public antenatal clinics in Gaborone, 2004–2008.

Methods Descriptive quantitative study using routinely collected antenatal data.

Results The overall syphilis prevalence amongst pregnant women in Gaborone decreased from 2.96% (95% CI, 2.55–3.37) in 2004 to 1.15% (95% CI, 0.89–1.41) in 2008 (p < 0.001), suggesting a significant downward trend in syphilis prevalence over a five years period. The age specific prevalence per total number of reactive VDRL/RPR was highest amongst pregnant women aged 26 to 30 years (p < 0.001) and lowest for those aged 16 to 20 years (p < 0.025) for 2004–2008, implying significant differences in the syphilis prevalence in each age group. However, the results reflect variations in syphilis prevalence rates within and between clinics.

There were slight fluctuations in the proportion of pregnant women screened for syphilis, ranged from 87.16% in 2004 to 91.20% in 2008. However, nearly all the clinics demonstrated no trends in the proportion of pregnant women screened for syphilis for 2004–2008.

Conclusion Syphilis sero-positivity in pregnancy in Gaborone has been declining for the last five years, but is far more prevalent amongst pregnant women aged 26 to 30 years and the lowest age specific prevalence was 16 to 20 years for 2004 to 2008. This decline may be attributed to a number of factors and in particular, the adoption of syndromic approach for management of sexually transmitted infections in all clinics across the country. This study showed variations in the trend of syphilis prevalence by clinics and proportions of pregnant women screened for syphilis. However, a high proportion of pregnant women not screened for syphilis may have contributed to under-estimate syphilis prevalence rates.