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Background: In response to a rising shortage of general practitioners (GPs), physicians in general internal medicine (GIM) have become part of the German primary care physician workforce. Previous studies have shown substantial differences in practice patterns between both specialties. The aim of this study was to analyse and compare the application of procedures by German GPs and GIM physicians based on routine data. Methods: The Association of Statutory Health Insurance Physicians in the federal state Schleswig-Holstein (Northern Germany) provided invoicing data of the first quarters of 2013 and 2015. Differences between GPs and GIM physicians in the implementation rate of 46 selected primary care procedures were examined by means of the Pearson χ2-test. The selection of procedures was based on international and own preliminary studies on primary care procedures. Results: In the first quarter of 2013/2015 respectively, 1228/1227 GPs and 447/484 GIM physicians provided services in Schleswig-Holstein. Significant differences were found for 20 of the 46 procedures. GPs had higher application rates of procedures concerning health screening (e.g. adolescent health examination, well-child visits) and minor surgery. GIM physicians more often applied technology-oriented procedures, such as ultrasound scans, electrocardiograms (ECG), and 24-h ambulatory blood pressure measurements. The treatment patterns of both specialities did not vary much during the study period. Cardiac stress testing was the only significantly increased GP procedure in that time. Conclusions: Our results suggest substantial differences in the application of procedures between GPs and GIM physicians with potential consequences for the overall primary healthcare provision. The findings could foster a discussion about training needs for procedures in primary care to ensure its comprehensiveness. The results reflect scope for changes in vocational training in the future for an effective and efficient re-allocation of primary healthcare. [ABSTRACT FROM AUTHOR]