Background: Essential hypertension is characterized by sympathovagal imbalance that is responsible for arrhythmias and sudden cardiac death. Antihypertensive drugs restores sympatho vagal balance. Losartan and amlodipine are common antihypertensive drugs. Objective: To compare the effect of losartan and amlodipine on heart rate variability (HRV) in hypertensive patients . Methods: This prospective analytical study was carried out in the Department of Physiology, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbag, Dhaka from July 2012 to June 2013. For this study, 120 newly diagnosed hypertensive patients without any treatment (group B, age 30-55 years) were selected from the Out Patients Department of cardiology, BSMMU, Dhaka on their first day of visit. 60 apparently healthy normotensive subjects were also studied as control (group A). HRV of the patients were measured both before and after they were treated with two different antihypertensive drugs (losartan and amlodipine) separately. According to the selection of drug these patients were divided into two groups. Group B1 included 60 patients received losartan 50 mg daily and group B2 included 60 patients treated by amlodipine 5 mg daily. They were observed once before the treatment (B1 a &B2 a) and after3 months medication(B1 b & B2 b ) and also after 6 months medication (B1 c & B2 c ). For assessing HRV, Mean heart rate (HR),Mean R-R interval, Max/Min R-R interval, SDNN, RMSSD were recorded by a polyrite. Data were compared among before treatment, after 3 months treatment and after 6 months treatment. For statistical analysis ANOVA, independent sample't' test and paired sample 't' were performed. Results: Mean resting pulse rate, mean heart rate, systolic blood pressure (SBP), diastolic blood pressure (DBP) were significantly higher(P<0.001) and mean R-R interval, SDNN, RMSSD were significantly lower(P<0.001) in patients before treatment compared to those of healthy normotensive subjects and to the values after treatment. In both drug groups, SDNN, RMSSD,mean R-R interval were found significantly higher after 6 months of treatment compared to their values after 3 months treatment and also close to the values in normotensive subjects. In losartan group RMSSD were found significantly higher (p<0.01) and mean R-R interval,SDNN were found though higher but not significant than the corresponding values in amlodipine treated patients after 6 months treatment. Conclusion: Vagal modulation is decreased in untreated hypertensive patients which is increased by treatment with both losartan and amlodipine but the effect is more pronounced in losartan. The decreased autonomic function was improved better with longer treatment duration.