Aim To determine the impact on clinical outcomes of specialist diabetes clinics compared with routine primary care clinics. Methods Observational study measuring clinical performance (process/outcome measures) in the primary care sector. A cohort of patients attending specialist diabetes clinics was compared with a control cohort of patients attending routine primary care clinics. Results Patients seen in specialist diabetes clinics had a significantly higher HbA1c than patients in routine primary care clinics (mean difference 0.58%; P < 0.001) but there was no significant difference in rate of improvement with visits compared with primary care clinics. In contrast, patients seen in the routine primary care clinics had significantly higher cholesterol levels (mean difference 0.24 mmol/l; P < 0.001) compared with patients in specialist diabetes clinics and their improvement was significantly greater over time (mean difference 0.14 mmol/l per visit compared with 0.10 mmol/l; P < 0.006). Patients in routine primary care clinics also had significantly higher diastolic blood pressure (mean difference 1.6 mmHg; P < 0.007) but there was no difference in improvement with time compared with specialist diabetes clinics. Uptake of podiatry and retinal screening was significantly lower in patients attending routine primary care clinics, but this difference disappeared with time, with significant increases in uptake in the primary care clinic group. Weight increased in both groups significantly with time, but more so in the specialist clinic patients (mean increase 0.18 kg per visit more compared with routine clinic primary care patients; P < 0.001). Conclusions This study provides evidence that the provision of primary care services for patients with diabetes, whether traditional general practitioner clinics or diabetes clinics run by general practitioners with special interests, is effective in reducing HbA1c, cholesterol and blood pressure. However, the same provision of care was unable to prevent increasing weight or creatinine over time. No evidence was found that patients in specialist clinics do better than patients in routine primary care clinics.