Objective:To study the pathological basis of right atrial fibrillation in rheumatic heart disease (RHD) patients with atrial fibrillation (AF). Methods: Twenty-nine patients with mitral valve replacement of RHD were divided into AF group (n= 13) and sinus rhythm group (SN group) (n= 16). There was no significant statistical difference in clinical factors between the 2 groups. During the operation of valve replacement, the samples of right atrial appendages were taken and the qualitative and quantitative study were made by light microscopy and electron microscopy. Results: (1) Light microscope: The interstitial fibrosis and the arrangement of myocardium was more disordered in AF group than that in SN group. However, no statistic difference was found in interstitial fibrosis and cellar hypertrophy degree between the 2 groups. (2) Electron microscope: Mitochondrial crosta broke and dissolved obviously in AF group. The mitochondrial volume in AF group was smaller than that in SN group. Volume density, average area and average perimeter in AF group were less than that in SN group; specific surface in AF group was bigger than that in SN group. There was significant difference of above factors between the 2 groups; but there was no significant difference of surface density and numerical density on area in the 2 groups. Volume density of myofibril in AF group and SN group were less than that in SN group. (3)Split of Intercalated disc(ID) gap was found in AF group, and there was marrowing and floccular substance in ID gap. Conclusion: There were significant differences in the pathological changes of right atrial myocardium between AF and SN with RHD, these changes may be the important pathological basis for RA fibrillation of AF patients with RHD.