Pneumococcal vaccination coverage of adults at risk for pneumococcal disease is below recommended levels. There is no observational data on pneumococcal vaccination and the incidence of lower respiratory tract infections in a general adult population. The current study had the objective to explore the incidence of lower respiratory tract infections and the pneumococcal vaccine coverage in function of age, influenza vaccination status and risk status, in Flanders, Belgium. We used data from Intego, ageneral practice-based morbidity registration network in Flanders (Belgium). We gathered data on pneumococcal vaccinations, influenza vaccination (in 2014) and ICPC2-coded diagnoses of pneumonia and acute bronchitis (2015). First, we divided the population into three groups along the risk status for developing apneumococcal infection according to the recommendations for pneumococcal vaccination in adults by the Belgian High Council of Health. 28.6% from our total adult study population are considered the target group for vaccination. Second, we found that the average pneumococcal vaccination coverage in this targeted population was 18.7%. Third, we found asignificantly higher incidence of LRTI in patients previously vaccinated against pneumococcal disease and/or influenza across the majority of subgroups. Pneumococcal vaccination coverage in Flanders is quantitatively low but observed to be qualitatively high in terms of reaching the most at risk population. Our findings are likely to be highly relevant to addressing future vaccination strategies in Flanders.