The aim of this study is to evaluate the agreement between three-dimensional (3D) transesophageal echocardiography (TEE) and multidetector computed tomography (MDCT) for assessing mitral annular (MA) dimensions. A total of 105 patients (79 ± 9 years old, 52% male) who underwent clinically indicated 3D TEE and MDCT feasible for MA geometrical assessment were included. Using dedicated semi-automated postprocessing software, MA geometry, including mitral annular area (MAA), perimeter, septal-lateral (SL) diameter, and inter-trigonal (TT) diameter, was evaluated using 3D TEE and MDCT. Compared to 3D TEE, MAA, perimeter, and SL distance measured on MDCT data were larger (9.9 ± 3.0 vs. 9.3 ± 3.1 cm2 for MAA; 115 ± 18 vs. 108 ± 18 mm for perimeter; and 35 ± 5 vs. 32 ± 5 cm for SL distance, all p < 0.001). By contrast, the TT distance was comparable between MDCT and 3D TEE (26 ± 4 vs. 26 ± 4 cm, p = 0.258). The correlations of all the MA dimensions were good to excellent between the two modalities (R = 0.911 for MAA, 0.890 for perimeter, 0.739 for TT distance, and 0.857 for SL distance, respectively, all p < 0.001). This study showed good agreement between 3D TEE- and MDCT-derived MA measurements although MDCT systematically provided larger MAA, perimeter, and SL distance compared with 3D TEE.