Purpose: Remarkable and uncontrollable changes with modification during pregnancy are connected with the autonomic control and consequently with the heart rate variability (HRV). Heart rate variability is a sum of different mechanisms and if pregnancy is a state of change, these modifications could be extracted from HRV analysis. Objective: To assess the effect of pregnancy on heart rate variability among pregnant mothers during first trimester of pregnancy and third trimester of pregnancy. Materials and Methods: HRV was measured for 5 minutes of continuous recording of electrocardiogram (ECG) lead II, using windows based HRV analysis system variowin-HR after obtaining permission from the Institutional Review Board of Government Medical College, Bhavnagar and written consent from 30 pregnant subjects and 30 non-pregnant control subjects at autonomic function lab, Dept of Physiology, Bhavnagar. Result: Frequency domain parameters, very low frequency (VLF), low frequency (LF), high frequency (HF) and HF normalized unit (nu) were significantly decreased and LF (nu) and LF/HF significantly increased in pregnant subject in 3rd trimester as compared to their 1st trimester of pregnancy. Time Domain parameters like SDNN, RMSSD, SDSD, NN50 count, pNN50, SD1/SD2, triangular HRV index and average R-R interval were significantly decreased during 3rd trimester of pregnancy. Conclusion: The inhibition of resting parasympathetic activity or vagal blockage and an increment of the sympathetic modulation during the 3rd third trimester of gestation in pregnancy as compared to their 1st trimester and healthy non-pregnant subjects. Sympathovagal imbalance and abnormally low HRV may more pronounce during later stage of normal pregnancy.