Anastomotic quality of coronary artery bypass grafting is directly associated with peri-operative and long-term clinical results. In this study, we investigated a cut-off value for intra-operative flow measurement. This value could be of use to a surgeon in determining the anastomotic quality of grafts. Intra-operative transit-time flow variables (mean flow, pulsatility index, % efficiency, fast Fourier transformation (FFT) of the flow curve) and the 2-week post-operative angiographic findings were examined in 66 coronary artery bypass grafts, including 33 internal thoracic arteries. There were significant differences between patent and non patent grafts in all of the intra-operative flow parameters. Only the FFT ratio, the ratio of powers of the fundamental frequency and its first harmonic, could be utilized as a cut-off value to distinguish patent from non patent grafts. All stenotic or occluded grafts showed an intra-operative FFT ratio of <1.0, while all patent grafts yielded a ratio of >1.0. Based upon these results, we concluded that power spectral analysis of flow measurement might be useful for intra-operative differential diagnosis of the anastomotic quality in coronary artery bypass grafting.