BACKGROUND: Cardiovascular morbidities have been reported in hypothyroidism. AIMS: The objective of this study is to investigate the link of sympathovagal imbalance (SVI) to cardiovascular risks (CVRs) and the plausible mechanisms of CVR in hypothyroidism. MATERIALS AND METHODS: Age-matched 104 females (50 controls, 54 hypothyroids) were recruited and their body mass index (BMI), cardiovascular parameters, autonomic function tests by spectral analysis of heart rate variability (HRV), heart rate response to standing, deep breathing and blood pressure response to isometric handgrip were studied. Thyroid profile, lipid profile, immunological and inflammatory markers were estimated and their association with low-frequency to the high-frequency ratio (LF-HF) of HRV, the marker of SVI was assessed by multivariate regression. RESULTS: Increased diastolic pressure, decreased HRV, increased LF-HF, dyslipidemia and increased high-sensitive C-reactive protein (hsCRP) were observed in hypothyroid patients and all these parameters had significant correlation with LF-HF. BMI had no significant association with LF-HF. Atherogenic index (beta 1.144, P = 0.001) and hsCRP (b 0.578, P = 0.009) had independent contribution to LF-HF. LF-HF could significantly predict hypertension status (odds ratio 2.05, confidence interval 1.110-5.352, P = 0.008) in hypothyroid subjects. CONCLUSIONS: SVI due to sympathetic activation and vagal withdrawal occurs in hypothyroidism. Dyslipidemia and low-grade inflammation, but not obesity contribute to SVI and SVI contributes to cardiovascular risks.