Many patients with diabetes do not achieve target values. One of the reasons for this is clinical inertia. The correct explanation of clinical inertia requires a conjunction of patient with physician and health care system factors. Our aim was to determine the rate of clinical inertia in treating diabetes in primary care and association of patient, physician, and health care setting factors with clinical inertia. This was a national, multicenter, observational, cross-sectional study in primary care in Croatia. Each family physician (FP) provided professional data and collected clinical data on 15-25 type 2 diabetes (T2DM) patients. Clinical inertia was defined as a consultation in which treatment change based on glycated hemoglobin (HbA1c) levels was indicated but did not occur. A total of 449 FPs (response rate 89.8%) collected data on 10275 patients. Mean clinical inertia per FP was 55.6% (SD ±26.17) of consultations. All of the FPs were clinically inert with some patients, and 9% of the FPs were clinically inert with all patients. The main factors associated with clinical inertia were: higher percentage of HbA1c, oral anti-diabetic drug initiated by diabetologist, increased postprandial glycemia and total cholesterol, physical inactivity of patient, and administration of drugs other than oral antidiabetics. Clinical inertia in treating patients with T2DM is a serious problem. Patients with worse glycemic control and those whose therapy was initiated by a diabetologist experience more clinical inertia. More research on causes of clinical inertia in treating patients with T2DM should be conducted to help achieve more effective diabetes control.