Objectives To describe and explore data from the surveillance of chlamydia, syphilis, gonorrhoea and genital warts by the Belgian Network of Sentinel General Practices (SGP) over the first 2 years (2013 and 2014) and to estimate the incidence of these 4 sexually transmitted infections (STIs). A special focus is put on data quality. Design Retrospective observational study. Setting General practices from the nationwide representative SGP network. Outcome measures Agreement between data distributions by year, agreement between SGP-based incidence and incidence based on mandatory notification, missingness of patient age or gender and incompleteness of sexual risk history of patients. Results 306 new STI episodes were reported from 298 patients, corresponding with an episode-based incidence of 91.9/100 000 (95% CI 81.9 to 102.8) general practice patients, with almost half of it due to chlamydia. The incidence of chlamydia in men was significantly higher in 2014 than in 2013. Population characteristics were similarly distributed in 2013 and 2014. The SGP-based incidence of gonorrhoea and syphilis in Flanders were in agreement with the incidence based on mandatory notification of cases. Patient age or gender was missing from 35 episodes (11.4%). Independent determinants of missingness of patient age or gender were the Flemish region (OR 3.46; 95% CI 1.02 to 11.73) and genital warts infection (OR 2.23; 95% CI 1.07 to 4.63). An incomplete sexual risk history was reported for 54.6% STI episodes. The odds for an incomplete sexual history were higher for older patients (OR 1.72; 95% CI 1.06 to 2.76) and for patients infected with syphilis, gonorrhoea or co-infection(s) (OR 1.71; 95% CI 1.03 to 2.83). Conclusions Incompleteness of reports about patients with STI sexual risk histories is important from the perspective of quality of data and of quality of care. Together with the low rates of both HIV testing and discussion of partner notification, this suggests that a general practice guideline is needed.