Background: We have recently shown how the combination of information from continuous glucose monitor (CGM) and heart rate variability (HRV) measurements can be used to construct an algorithm for prediction of hypoglycemia in both bedbound and active patients with type 1 diabetes (T1D). Questions remain on how cardiovascular autonomic neuropathy (CAN) influences these measurable changes. This study aims to examine if changes in HRV during hypoglycemia are confounded by the presence of CAN. Methods: Twenty-one adults (hereof 13 men) with T1D prone to hypoglycemia were recruited and monitored with CGM and a Holter device while they performed normal daily activities. CAN was diagnosed using two cardiac reflex tests: (1) deep breathing and (2) orthostatic hypotension and end organ symptoms. Early CAN was defined as the presence of one abnormal reflex test and severe CAN was defined as two abnormal tests or one abnormal test combined with symptoms of autonomic neuropathy. Results: A total of 19 hypoglycemic and corresponding euglycemia periods were identified among the 21 patients. Eleven patients were diagnosed with CAN, hereof five with severe CAN. The HRV parameter low frequency (LF) was significantly (P = 0.029) reduced during hypoglycemia. Changes in LF during hypoglycemia were not different between patients with and without CAN, -0.64 versus -0.48 log(LF) (P = 0.74). Conclusions: Our data show that there are measurable changes in HRV during hypoglycemia, and present in both patients with and without CAN.