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Laser Doppler perfusion monitoring is a suitable method for microvascular blood perfusion measurements. When used on a moving tissue or organ, the Doppler signal arising from the moving blood cells may be distorted. ECG triggering of the laser Doppler signal can be used for reducing the influence from movements during measurements on the beating heart. The aim of this study was to determine the most appropriate triggering intervals during the cardiac cycle for online measurements. Recordings from thirteen coronary artery bypass graft (CABG) patients were included in the study. During surgery, the fibre-optic probe was passed through the chest wall and sutured to the left anterior ventricular wall with the probe tip inserted 3–5 mm into the myocardium. After the patient arrived at the intensive care unit a second measurement was initiated and lasted for about two hours. Before the probe was removed a third measurement was performed for about 5 minutes the following morning. A total of 97 data sequences were analysed and the intervals of low and stable perfusion signal were compared to the positions of the T and P peaks in the ECG. It was found that the most appropriate time intervals were in late systole at the T peak [−3, 9] ms and just before the P peak [−28, -10] ms in late diastole. However, the position of these intervals may vary between individuals, because of e.g., abnormal cardiac motion. With the use of the appropriate interval online measurement of the myocardial perfusion on a beating heart appears possible.