Background: Hypothyroidism is associated with autonomic dysfunction and oxidative stress. Slow breathing exercise (SBE), a yoga-based relaxation technique, improves cardiac autonomic nerve function by changing sympathetic or parasympathetic activity. Objective: To assess the effect of SBEon cardiac autonomic tone and in hypothyroid patients. Methods: This non randomized controlled trial was conducted on 50 newly diagnosed drug naive female hypothyroid patients (18-45 years of age)recruited from the outpatient department of the Department of Endocrinology, Bangabandhu Sheikh Mujib Medical University,(BSMMU), Shahbag, Dhaka. Twenty five apparently healthy female subjects formed control group. . Among the 50 hypothyroid patients, 25 were consecutively assigned with SBE for 90 days (Group SBE) and the remaining 25 patients were without SBE and followed up after 90 days (Group NSBE). Both groups of patients received treatment with thyroid hormone replacement during their follow up period. Control group did not perform SBE or any other exercise. Data were recorded at baseline(Day 0) and after 90 days in all the subjects. Based on data recording period SBE group was designated as SBE0(at day 0 or pre intervention)and SBE90(at day 90 or post intervention). Similarly, NSBE0(day 0) and NSBE90 (day 90) and control group was also designated as control0 (day 0) and control90 (day 90).Resting cardic autonomic tonic activity was assessed by frequency domain analysis of Heart Rate Variability(HRV). HRV data were recorded by a digital data acquisition device Power Lab, AD Instrument Australia. Data were expressed as mean±SD. For statistical analysis, ANOVA followed by post hoc Bonferroni test and paired sample “t” test were done. Results: At baseline i.e. at day 0 before follow up, diastolic blood pressure (DBP) (p<0.05), low frequency in normalized unit (LF norm) (p<0.001), low frequency/high frequency ratio (LF/HF) (p<0.001) were significantly higher and total power (TP) (p<0.001), low frequency power (LF power) (p<0.01), high frequency power (HF power) (p<0.001), high frequency power in normalized unit (HF norm) (p<0.001) were significantly lower in hypothyroid patients (group SBE0and NSBE0 ) compared to healthy control (group control0). After 90 days of intervention with SBE, SBP, DBP, LF norm, LF/HF ratio decreased significantly and TP, HF power, HF norm increased significantly in group SBE90 compared to SBE0. Whereas, in group NSBE90, after 90 days of follow up, LF norm, LF/HF ratio decreased significantly and HF power, HF norm increased significantly compared to NSBE0. Again, after 90 days of follow up/SBEHF norm were significantly higher and LF norm, LF/HF ratio were significantly lower in SBE90 compared to NSBE90. In addition, significant difference was present in all these parameters between NSBE90 and control90. Also, after 90 days of SBELF norm, HF norm and LF/HF ratio was not significantly different from control. Conclusions: Based on these results, it can be concluded that autonomic dysfunction characterized by reduced vagal tone and sympathetic hyperactivity occurred in drug naïve hypothyroid patients. In addition, thyroid hormone replacement therapy improved autonomic dysfunction by increasing parasympathetic and decreasing sympathetic tonic activity. Moreover, SBE caused further improvement of autonomic dysfunction and could restore sympathovagal balance to its normal state in these patients. J Bangladesh Soc Physiol 2023;18(1): 9-18