Background Somatotype is a quantified expression of the morphological conformation of a person in terms of three-numeral rating each representing one component; fat (endomorphy), muscle mass (mesomorphy) and bone length (ectomorphy) in the same order. Certain somatotypes are more prone to develop the particular disease. Obesity and overweight are already epidemic among Indian adolescents and are increasing at an alarming rate, and obesity is linked to cardiovascular (CV) risk in this age group. Identifying the heart rate variability (HRV) is an established non-invasive test to identify the CV risk. The objective of this study is to record the HRV data for each somatotype category and to compare the HRV data among these somatotype categories in adolescents. Methods The volunteer adolescents in the age group of 12-17 years were classified into a different somatotyping categories based on the Heath Carter somatotyping method. The short-term HRV was recorded in all the subjects using wireless BioHarness 3.0. Results Based on the time domain and frequency domain parameters, the parasympathetic activity showed decreasing order as follows: central>ectomorphy>mesomorphy>endomorphy, whereas sympathetic activity showed increasing order as follows: central<ectomorphy<mesomorphy<endomorphy in both boys and girls. Girls have higher parasympathetic activity and lesser sympathetic activity than boys in ectomorphy and mesomorphy. In the central somatotype and endomorphy categories, genders were comparable. Conclusion Our study suggests that endomorphy and mesomorphy have poorer autonomic tone when compared to other somatotype categories.