Despite having almost identical origins and similar perfusion pressures, the flow velocity waveforms in the left and right coronary arteries are strikingly different. We hypothesized that pressure differences originating from the distal (microcirculatory) bed would account for the differences in the flow velocity waveform. We used wave intensity analysis to separate and quantify proximal- and distal- originating pressures, to study the differences in velocity waveforms. In 20 subjects with unobstructed coronary arteries, sensor-tipped intra-arterial wires were used to measure simultaneous pressure and Doppler velocity in the proximal left main stem (LMS) and proximal right coronary artery (RCA). Proximal- and distal-originating waves were separated using wave intensity analysis and differences in waves were examined in relation to structural and anatomical differences between the two arteries. Diastolic flow velocity was lower in the RCA than in the LMS (35.1±21.4cm/s versus 56.4±32.5cm/s, p<0.002) and consequently the diastolic-systolic ratio of peak flow velocity in the RCA was significantly less than the LMS (1.00±0.32 versus 1.79±0.48, p<0.001). This was due to a lower distal-originating suction wave (8.2±6.6 x10³Wm^-2s^-1versus 16.0±12.2 x103Wm-2s^-1, p<0.01). The suction wave in the LMS correlated positively with left ventricular pressure (r=0.6, p<0.01) and in the RCA with estimated right ventricular systolic pressure (r=0.7, p=0.05) but not with the respective diameter in these arteries. In contrast to the LMS, where coronary flow velocity was predominantly diastolic, in the proximal RCA coronary flow velocity was similar in systole and diastole. This difference was due to a smaller distal-originating 'suction wave' in the RCA which can be explained by differences in elastance and pressure generated between right and left ventricles.