The aim of the study was to assess the accuracy of the three-dimensional (3D) quantitative coronary analysis (QCA) system by comparing with that of intravascular ultrasound (IVUS) QCA and two-dimensional (2D) QCA. 3D QCA, 2D QCA and IVUS QCA were performed in 45 vessel segments. The obtained values for the branch to branch segment vessel length and the proximal part of the segment vessel's lumen diameter were measured. Inter-technique agreement was analyzed using paired sample t-test and Bland-Altman analysis. No differences were found in vessel lengths taken by 3D QCA and IVUS QCA (mean difference: 0.29 ± 1.06 mm, P = 0.07). When compared with IVUS QCA, 2D QCA underestimated vessel length (mean difference: -1.78 ± 2.55, P < 0.001). Bland-Altman analysis showed close agreement and a small bias between 3D QCA and IVUS QCA in the measurement of vessel length. The vessel lumen diameter measurements by 2D QCA and 3D QCA were significantly lower than that by IVUS QCA (mean difference: -0.64 ± 0.69, P < 0.001; -0.56 ± 0.52, P < 0.001 respectively). Rotational angiography with 3D reconstruction can provide a more accurate vessel length measurement, whereas 2D and 3D QCA underestimated the vessel lumen diameter compared with IVUS QCA.