The geometry of coronary arteries affects regional atherogenic processes. Accurate images can be assessed using multislice computer tomography (MSCT) to estimate bifurcations angles. We propose a three-dimensional (3D) method to measure true bifurcation angles of coronary arteries and to determine possible correlations between plaque presence and angulations. The left main (LM) coronary artery, left anterior descendent (LAD) and left circumflex artery (LCX) were imaged in 40 atherosclerotic and 35 healthy patients, using 64-rows MSCT. This Y-junction was simplified fitting a 3D cylinder to each vessel to estimate true bifurcation angles and diameters. The method was tested in phantoms and interobserver variability was assessed. Geometrical results were compared between groups using an unpaired t-test. The cylinders fitted reasonably well with mean distances to measured points below 0.4 mm. LAD-LCX bifurcation angles were wider in the atherosclerotic group (p < 0.01). LAD (p < 0.01) and LCX (p < 0.05) diameters were also larger. In phantoms mean absolute difference between true and estimated angles (N = 27) was 0.44 +/- 0.54 degrees . Interobserver mean difference (N = 135) was 1.8 +/- 5.8 degrees . Simplifying coronary bifurcation with cylinders results in a reliable technique to assess coronary artery geometry in 3D, avoiding planar projections and decreasing interobserver variability. Geometrical risk factors should be incorporated to properly predict atherosclerosis processes.