While heart rate variability (HRV) is an established marker of cardiovascular health, the extent to which continuously measured HRV changes over time and the relationship between these changes and clinical outcomes are less clear. We performed a health system analysis of 225 patients implanted with a cardiac defibrillator or cardiac resynchronization device (CRT) with continuous HRV recording capabilities. We found that continuously measured HRV changed modestly over 2 years. Low baseline HRV, which is associated with low parasympathetic tone and/or increases in sympathetic tone, pertains a worse clinical prognosis as reflected by a significant association with all-cause hospitalization. Observed changes in HRV over 6-months of follow-up were not associated with subsequent outcomes.