Background: In an industrialised and modernized society, individuals tend to perform less physical work and non-communicable diseases therefore become more prevalent. A major problem of the sedentary lifestyle adopted due to modernization is a sympathovagal imbalance. Exercise can affect this imbalance. Sympathovagal imbalance can be easily assessed by determining the heart rate variability (HRV). Aim: To compare the short term heart rate variability (HRV) of regularly exercising and nonexercising young adults. Material and methods: This cross-sectional study was conducted in the Department of Physiology of Coimbatore Medical College, Coimbatore. Participants included 30 regularly exercising (Group I) and 30 nonexercising young adults (Group II) aged 18-20 years. After taking informed consent, a 5 minute lead II electrocardiogram (ECG) was acquired and digitized at the rate of 1000 samples per second and HRV analysis was done. Statistical analysis was done using the unpaired Student's t-test. Results: There was a significant difference between the LF/HF ratio and HFnu values of exercising and non exercising young adults (p value <0.0001), the LF/HF ratios being higher and the HFnu values being lower in the nonexercising group There was however no significant difference between their LFnu values (p value = 0.0836). The body mass index (BMI) was 22.52 ± 1 and 25.33 ± 2.2 in exercising and nonexercising young adults respectively. Conclusion: In this study, we found a significant difference between the LF/HF ratio and HFnu values of exercising and non exercising young adults. The sympathovagal imbalance among nonexercising young adults could possibly be corrected by life style modification.