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The aim of this study was to identify associations of the parameters of heart rate variability (HRV) with the variations in geomagnetic activity (GMA), solar wind, and cosmic ray intensity (CRI) in patients after coronary artery bypass grafting or valve surgery in Kaunas, Lithuania, during 2008–2012. The data from 5-minute electrocardiograms (ECGs) in 220 patients were used. ECGs were carried out at 1.5 months, 1 year, and 2 years after the surgery (N = 495). A lower (higher) very-low-frequency-band (VLF) and a higher (lower) high-frequency band (HF) in normalised units (n.u.) were associated with a low maximal daily 3-hourly ap (the DST index > 1). A lower mean standard deviation of beat-to-beat intervals (SDNN) and VLF, LF, and HF powers were lower in patients when Ap < 8 occurred two days after the surgery, and a low solar wind speed (SWS) occurred two days before the ECG. The effect of CRI was non-significant if the linear trend was included in the model. Low GMA and a low SWS may effect some HRV variables in patients after open-heart surgery. The GMA during the surgery may affect the SDNN in short-term ECG during the longer period. [ABSTRACT FROM AUTHOR]