Shape irregularities of intracranial aneurysms may indicate an increased risk of rupture. To quantify morphological differences, Fourier analysis of the shape of intracranial aneurysms was introduced. We compared the morphology of 45 unruptured (UIA) and 46 ruptured intracranial aneurysms (RIA) in 70 consecutive patients on the basis of 3D-rotational angiography. Fourier analysis, coefficient of roundness and qualitative shape assessment were determined for each aneurysm. Morphometric analysis revealed significantly smaller coefficient of roundness (P < 0.02) and higher values for Fourier amplitudes numbers 2, 3 and 7 (P < 0.01) in the RIA group, indicating more complex and irregular morphology in RIA. Qualitative assessment from 3D-reconstructions showed surface irregularities in 78% of RIA and 42% of UIA (P < 0.05). Our data have shown significant differences in shape between RIA and UIA, and further developments of Fourier analysis may provide an objective factor for the assessment of the risk of rupture.