The present study was aimed to compare the left atrial and left ventricular diastolic functions amongst the rheumatic and degenerative mitral valve disease patients in atrial fibrillation who reverted to normal sinus rhythm following Cox-maze procedure. We prospectively investigated the left atrial and left ventricular function with Doppler echocardiography, by dividing into the rheumatic (N = 105) and the degenerative group (N = 47). Over the follow-up period (mean: 4.4 ± 1.2 years in the rheumatic group, 4.8 ± 1.3 years in the degenerative group), the rheumatic group showed statistically significant decrease in A' velocity and E' velocity, on contrary to degenerative group (A' velocity: mean decrease of 0.43 ± 0.13 cm/s in the rheumatic group, mean increase of 0.57 ± 0.11 cm/s in the degenerative group, p = 0.029, E' velocity: mean decrease of 0.23 ± 0.17 cm/s in the rheumatic group, mean increase of 0.21 ± 0.15 cm/s in the degenerative group, p = 0.031). In addition, the rheumatic group showed statistically significant increase in E/E' ratio than the degenerative group (mean increase of 4.49 ± 1.98 in the rheumatic group, mean increase of 1.74 ± 1.52 in the degenerative group, p = 0.047). Despite successful sinus rhythm restoration, the progressive loss of LA function as well as LV diastolic function is more prominent in the rheumatic group than the degenerative group. Therefore, differentiated strategies for postoperative surveillance are needed according to the pathology of mitral valve disease.