Background: Point-of-care testing (POCT) of HbA1c may result in improved diabetic control, better patient outcomes, and enhanced clinical efficiency with fewer patient visits and subsequent reductions in costs. In 2008, the Danish regulators created a framework agreement regarding a new fee-for-service fee for the remuneration of POCT of HbA1c in general practice. According to secondary research, only the Capital Region of Denmark has allowed GPs to use this new incentive for POCT. The aim of this study is to use patient data to characterize patients with diabetes who have received POCT of HbA1c and analyze the variation in the use of POCT of HbA1c among patients with diabetes in Danish general practice. Methods: We use register data from the Danish Drug Register, the Danish Health Service Register and the National Patient Register from the year 2011 to define a population of 44,981 patients with diabetes (type 1 and type 2 but not patients with gestational diabetes) from the Capital Region. The POCT fee is used to measure the amount of POCT of HbA1c among patients with diabetes. Next, we apply descriptive statistics and multilevel logistic regression to analyze variation in the prevalence of POCT at the patient and clinic level. We include patient characteristics such as gender, age, socioeconomic markers, health care utilization, case mix markers, and municipality classifications. Results: The proportion of patients who received POCT was 14.1% and the proportion of clinics which were “POCT clinics” was 26.9%. There were variations in the use of POCT across clinics and patients. A part of the described variation can be explained by patient characteristics. Male gender, age differences (older age), short education, and other ethnicity imply significantly higher odds for POCT. High patient costs in general practice and other parts of primary care also imply higher odds for POCT. In contrast, high patient costs for drugs and/or morbidity in terms of the Charlson Comorbidity index mean lower odds for POCT. The frequency of patients with diabetes per 1000 patients was larger in POCT clinics than Non-POCT clinics. A total of 22.5% of the unexplained variability was related to GP clinics. Conclusions: This study demonstrates variation in the use of POCT which can be explained by patient characteristics such as demographic, socioeconomic, and case mix markers. However, it appears relevant to reassess the system for POCT. Further studies are warranted in order to assess the impacts of POCT of HbA1c on health care outcomes.