Aims Hyperglycemia as evaluated by HbA1c is a risk factor for the development of cardiovascular autonomic neuropathy (CAN). The aim of the present study was to investigate whether continuous glucose monitoring (CGM) may add information beyond HbA1c in patients with type 2 diabetes and CAN. Methods 81 patients with type 2 diabetes (43 men, mean age 58 ± 11 year, HbA1c 6.6 ± 0.5%). Patients were tested for CAN using cardiovascular reflex tests (response to standing, deep breathing and Valsalva maneuver) and underwent CGM for three days. CAN was defined as early (one test abnormal), or manifest (two or three tests abnormal). Results Twenty patients had early CAN and two patients had manifest CAN. Blood pressure, HbA1c, cholesterol levels and smoking habits were comparable in patients with vs. without CAN. Post-breakfast glycemic peak was significantly higher in patients with CAN (peak 207 vs 176 mg/dL, P = 0.009). Furthermore, the nocturnal glucose drop and dawn glucose was significantly higher in patients with CAN compared with patients without CAN (mean 134 vs. 118 mg/dL, P = 0.017 and mean 143 vs. 130 mg/dL, P = 0.045, respectively). Removing the two patients with manifest CAN from the statistical analysis didn't change the results. Conclusions These findings emphasize the importance of monitoring glucose patterns over 24-h and not only rely on HbA1c as therapeutic target in patients with type 2 diabetes and CAN.