Background The German Committee on Vaccination recommends pneumococcal vaccination for infants, seniors 60+ years and patients at risk with defined underlying diseases. Aim of this study was to assess the pneumococcal vaccination rate (pnc-VR) in patients with certain incident inherited or acquired immunodeficiency or immunosuppression and to understand who vaccinates these patients who are particularly at high risk to develop a pneumococcal infection. Methods We conducted a cohort study in patients aged 2 years or older, with a first episode of a "high-risk" condition between January 2013 and December 2014 based on a representative sample of German claims data. Pnc-VR was calculated as the proportion of patients receiving any pneumococcal vaccine within two years after first episode of "high-risk" condition. Further analyses cover pnc-VR stratified by high risk conditions and region, time to vaccination, and physician specialty administering the pneumococcal vaccination. Results The study population comprised 204,088 incident "high-risk" patients (56% female). The overall pnc-VR within two years was 4.4% (95%-confidence interval: 4.3%-4.5%). Within specific high-risk conditions, we found the highest vaccination rate of 11.5% (10.1%-13.0%) among patients starting immunosuppressants with underlying rheumatoid arthritis followed by 9.9% (7.8%-12.4%) in HIV patients. Stratification by region revealed a slightly higher vaccination rate in Eastern (6.5%: 6.0%-6.9%) compared to Western Germany (4.2%: 4.1-4.3%). Median time to vaccination within the first two years in vaccinated patients was 332.5 days (Q1 142 days, Q3 528 days). The majority of patients (92.6%) got vaccinated by a general practitioner. Conclusion Although these vulnerable patients need protection most, our study suggests that the overall pnc-VR after a first episode of a high-risk condition for pneumococcal disease is very low and vaccination is far too late. To prevent pneumococcal disease in patients at high risk, further efforts are needed to increase awareness and improve the timeliness of pneumococcal vaccination.