We aimed at evaluating the possible role of choroidal perfusion abnormalities in the development of choroidal neovascularisation (CNV) in patients with age-related macular degeneration (AMD). Twenty-six patients who had non-exudative AMD in the first eye and CNV secondary to AMD in the fellow eye were enrolled. Blood flow velocities, vessel pulsatilities and resistivities were measured from ophthalmic artery, nasal and temporal posterior ciliary arteries using colour Doppler imaging. Systolic and diastolic velocities were lower in eyes with CNV for all vessels, except for the systolic velocity of the nasal posterior ciliary artery (p >0.05). Pulsatility and resistivity indices were higher in eyes with CNV for all vessels. This difference was statistically significant for the resistivity index of the nasal and temporal posterior ciliary arteries (p = 0.032 and p = 0.021, respectively) and the pulsatility index of the nasal posterior ciliary artery (p = 0.035). We have shown that in patients with AMD choroidal blood flow is more impaired in the eyes with CNV than in the fellow eyes.