Background: Students getting admitted in private medical colleges belong to rich affluent family background. They tend to consume relatively high calories compared to physical output, leading to significant weight gain overtime. Objective:-Study objective was to find the association between heart rate variability and obesity in obese medical students. Materials and Methods:-A cross sectional study of one forty eight medical and dental students was conducted. They were screened for body mass index. The students were divided into three groups according to WHO technical series 854 recommended cut off values. An ECG is recorded continuously throughout the period of deep breathing. The result is then expressed as the mean of the difference between maximum and minimum heart rates for the six measured cycles in beats per minute. A difference of ? 15 beats/min (normal), 11 -14 beats/min (borderline), and values of ?10 beats/min (abnormal). Results:-Among students with BMI cut off value __ampersandsignlt;50th percentile, 28(87.5%) and 4(12.5%) had normal and mild HRV values respectively. Students with BMI cut off value 50th-85th percentile, 64(94.1%) had normal and 4(5.9%) had mild HRV values. The students with BMI cut off value __ampersandsigngt;85th percentile, 31(96.9%) and 1(3.1%) had normal and mild values respectively. Majority of male students [96.2 %( n= 50)] and female [91.2 %(n=73) ]showed normal HRV values. Conclusion:- In this study, there was no association between obesity and heart rate variability. The gender did not appear to be related to heart rate variability during deep breathing.