Background: The number of newly diagnosed gonorrhoea and syphilis cases has increased in Flanders in recent years. Our aim was to investigate, to which extent these diagnoses were registered by general practitioners (GPs), and to examine opportunities and limits of the Intego database in this regard. Methods: Data from a retrospective cohort study based on the Flemish Intego general practice database was analyzed for the years 2009–2013. Case definitions were applied. Due to small case numbers obtained, cases were pooled and averaged over the observation period. Frequencies were compared with those calculated from figures of mandatory notification. Results: A total of 91 gonorrhoea and 23 syphilis cases were registered. The average Intego annual frequency of gonorrhoea cases obtained was 11.9 (95% Poisson confidence interval (CI) 9.6; 14.7) per 100,000 population, and for syphilis 3.0 (CI 1.9; 4.5), respectively, while mandatory notification was calculated at 14.0 (CI: 13.6, 14.4) and 7.0 (CI: 6.7, 7.3), respectively. Conclusion: In spite of limitations such as small numbers and different case definitions, comparison with mandatory notification suggests that the GP was involved in the large majority of gonorrhoea cases, while the majority of new syphilis cases did not come to the knowledge of the GP.