Background: Although ocular tonography measures a pulsatile component of the ocular perfusion, the retinal and/or choroidal components of this pulsatile flow remain undefined. Aim: To compare ocular tonography with the assessment of flow velocities in arteries supplying the retina, choroid and entire orbit. Methods: 22 normal eyes from 11 subjects were studied. Pulsatile ocular blood flow (POBF) was measured using the ocular blood flow tonograph, and flow velocities in the ophthalmic, central retinal (CRA) and temporal short posterior ciliary arteries (TSPCA) using colour Doppler imaging. The correlation between POBF and retrobulbar flow velocities was determined. Results: POBF correlated significantly with peak systolic velocity (PSV) of the CRA (r = 0.56, p = 0.007) and the TSPCA (r = 0.48, p = 0.02), and with the resistive index of the TSPCA (r = 0.45, p = 0.04). Additionally, pulse amplitude (PSV - end diastolic velocity) in the CRA and the TSPCA correlated significantly with POBF measurements (each p<0.05). However, POBF did not correlate with any flow velocity indices in the ophthalmic artery. Conclusion: POBF is associated with systolic and pulsatile components of blood flow velocities in both the CRA and the TSPCA. This result suggests that POBF determinations are influenced by the pulsatile components of both choroidal and retinal perfusion.