BACKGROUND: Solar and geomagnetic activity (GA) have been linked to increased cardiovascular (CVD) events. We hypothesize that heart rate variability (HRV) may be the biological mechanism between increased CVD risk and intense geomagnetic disturbances (GMD). METHODS: To evaluate the impact of GA and intense GMD on HRV in 809 elderly men [age mean 74.5 (SD = 6.8)] enrolled in the Normative Aging Study (Greater Boston Area), we performed repeated-measures using mixed-effects regression models. We evaluated two HRV outcomes: the square root of the mean squared differences of successive normal-to-normal intervals (r-MSSD) and the standard deviation of normal-to-normal heartbeat intervals (SDNN) in milliseconds (ms). We also compared the associations between K(p) and HRV in patients with and without comorbidities such as diabetes and coronary heart diseases (CHD). We used data on global planetary K-Index (K(p)) from middle latitudes as a GA and GMD (>75th K(p)) parameters from the National Oceanic and Atmospheric Agency\'s Space Weather Prediction Center. RESULTS: We found a near immediate effect of continuous and higher K(p) on reduced HRV for exposures up to 24 h prior to electrocardiogram recording. A 75th percentile increase in 15-hour K(p) prior the examination was associated with a -14.7 ms change in r-MSSD (95 CI: -23.1, -6.3, p-value = 0.0007) and a -8.2 ms change in SDNN (95 CI: -13.9, -2.5, p-value = 0.006). The associations remained similar after adjusting the models for air pollutants over the exposure window prior to the event. In periods of intense GMD, the associations were stronger in patients with CHD and non-diabetes. CONCLUSIONS: This is the first study to demonstrate the potential adverse effects of geomagnetic activity on reduced heart rate variability in a large epidemiologic cohort over an extended period, which may have important clinical implications among different populations.