Background: Left atrial (LA) dilatation in patients with atrial fibrillation (AF) can induce functional mitral regurgitation (MR) despite a preserved left ventricular ejection fraction (LVEF). The purpose of this study was to investigate the etiology of this functional MR. Methods: We retrospectively examined clinical and echocardiographic data from 5,202 consecutive cases that underwent transthoracic echocardiography. AF appeared in 544 patients, and we selected 159 with AF and LVEF ≥50% after excluding patients with other underlying heart diseases. Results: Significant (moderate or greater) degrees of functional MR were seen in 13 (8.2%) patients and were more frequently seen in patients with an AF duration of >10 years than in others (27 vs. 4%, p = 0.0057). Multiple regression analysis revealed that both the LA dimension index and the left ventricular (LV) systolic dimension index were independent determinants of the MR grading. Among the mitral morphologic parameters, the mitral annular (MA) dimension index and the hamstringing phenomenon of the posterior mitral leaflet were independent determinants of MR grading. Significant MR was not seen in patients without LA dilatations, but it occurred in 14% of patients with LA dilatation alone and in 55% with both LA and LV dilatations; the MA dimension index increased in this order. Conclusions: The grading of functional MR occurring in patients with AF and preserved LVEF depends on both the LA dimension and the LV systolic dimension. The MR grading also depends on both the MA dilatation and the hamstringing phenomenon of the posterior mitral leaflet.