Wall shear stress, the force per areaacting on the lumen wall due to the blood flow, isan important biomechanical parameter in the localizationand progression of atherosclerosis. To calculateshear stress and relate it to atherosclerosis, a3D description of the lumen and vessel wall isrequired. We present a framework to obtain the 3Dreconstruction of human coronary arteries by thefusion of intravascular ultrasound (IVUS) and coronarycomputed tomography angiography (CT). Weimaged 23 patients with IVUS and CT. The imagesfrom both modalities were registered for 35 arteries,using bifurcations as landmarks. The IVUS imagestogether with IVUS derived lumen and wall contourswere positioned on the 3D centerline, whichwas derived from CT. The resulting 3D lumen andwall contours were transformed to a surface forcalculation of shear stress and plaque thickness. Weapplied variations in selection of landmarks andinvestigated whether these variations influenced therelation between shear stress and plaque thickness.Fusion was successfully achieved in 31 of the 35arteries. The average length of the fused segmentswas 36.4 ± 15.7 mm. The length in IVUS and CTof the fused parts correlated excellently (R2 = 0.98).Both for a mildly diseased and a very diseasedcoronary artery, shear stress was calculated andrelated to plaque thickness. Variations in the selectionof the landmarks for these two arteries did notaffect the relationship between shear stress andplaque thickness. This new framework can thereforesuccessfully be applied for shear stress analysis inhuman coronary arteries.