Background: Previously our research findings revealed that low heart rate variability, a measure of autonomic imbalance, is associated with increased incidence of coronary heart disease (CHD) and heart failure (HF) in a cohort of post-menopausal women. Since CHD is strongly associated with HF, we investigated the effect of CHD on relationship of HRV and HF subtypes, i.e., heart failure with reduced ejection fraction (HFrEF) and heart failure with preserved ejection fraction (HFpEF), in post-menopausal women. Methods: Total of 28,603 post-menopausal women free of baseline CHD, HF and cardiac arrhythmias enrolled in Women’s Health Initiative (WHI) study, were followed for incident hospitalized CHD, HF and its subtypes (HFrEF vs HFpEF). Using multivariate cox proportional hazard model, we estimated the association of above outcomes with baseline quartiles of HRV measures; SDNN (standard deviation of normal-to-normal RR interval) and RMSSD (root mean square of successive difference of RR interval) produced by 10-second twelve-lead ECG on enrollment. We then evaluated the relationship between HRV and HF subtypes stratified by incident CHD. Results: A total of 2279 incident CHD and 1562 incident HF events occurred during a median follow-up duration of 17.5 years. After adjusting for incident CHD in a multivariate cox proportional model, association of low SDNN and RMSSD with incident HF remained significant (SDNN HR 1.19, CI 1.05 - 1.35; RMSSD HR 1.13 (1.00 - 1.29). However, in stratified analysis low SDNN was associated with increased incidence of HFpEF only among participants without incident CHD (HR 1.29, CI 1.05 - 1.58) and not in those with incident CHD (HR 1.06, CI 0.77 - 1.47). Whereas low SDNN was associated with increased incidence of HFrEF only among participants with incident CHD (HR 1.44. CI 1.05 - 1.98) and not in those without incident CHD (HR 1.18, CI 0.87 - 1.61). Conclusion: Post-menopausal women with low HRV who develop CHD have an increased risk of HFrEF while those who don’t develop CHD have an increased risk of HFpEF. The relationship between autonomic imbalance and HF subtypes is dependent on CHD status.