In clinical practice, heart rate variability (HRV) has not been considered an indicator for the preventive assessment of cardiovascular autonomic neuropathy (CAN). The paper studies HRV in a large, randomly selected group. A cross-sectional study included a representative sample of 5707 Kazakhs aged 20 years and older from a total population of 25,454 attached to an urban clinic in the capital of Kazakhstan. The sample was drawn from individuals who visited the clinic for a preventive examination. CAN diagnosis was confirmed using data from questionnaires, electronic medical records, HRV, and heart rate measurements. Mean values of the standard deviation of normal sinus RR intervals (SDNN) and the root mean square of successive RR interval differences (RMSSDs) from a 24 h electrocardiogram recording were assessed. CAN was identified in 17.19% of the study participants, with a ratio of the subclinical to clinical phase of 1:0.24. Diabetes mellitus was present in 30.99% of patients with CAN. The prevalence of CAN varied by sex and age, aligning with the prevalence trajectory of diabetes. It was concluded that the SDNN and RMSSD parameters in electrocardiographic studies can be used for preventive measures in the context of limited healthcare resources.