To quantify valvular morphological assessment, some two-dimensional (2D) and three-dimensional (3D) scoring systems have been developed to target the patients for balloon mitral valvuloplasty; however, each scoring system has some potential limitations. To achieve the best scoring system with the most features and the least restrictions, it is necessary to check the degree of overlap of these systems. Also the factors related to the accuracy of these systems should be studied. We aimed to determine the correlation between the 2D Wilkins and real-time transesophageal three-dimensional (RT3D-TEE) scoring systems. This cross-sectional study was performed on 156 patients with moderate to severe mitral stenosis who were candidates for percutaneous balloon valvuloplasty. To morphologic assessment of mitral valve, patients were examined by 2D-transthoracic echocardiography and RT3D-TEE techniques on the same day. A strong association was found between total Wilkins and total RT3D-TEE scores (r = 0.809, p < 0.001). The mean mitral valve area assessed by the 2D and 3D was 1.07 ± 0.25 and 1.03 ± 0.26, respectively, indicating a mean difference of 0.037 cm2 (p = 0.001). We found a strong correlation between the values of mitral valve area assessed by 2D and 3D techniques (r = 0.846, p < 0.001). There is a high correlation between the two scoring systems in terms of evaluating dominant morphological features. Partially, mitral valve area overestimation in the 2D-transthoracic echocardiography and its inability to assess commissural involvement as well as its dependence on patient age were exceptions in this study.