The natural history of uncomplicated mitral valve prolapse (MVP) is not clearly understood. To determine the site-related differences in regression and progression of MVP, 112 patients with idiopathic MVP were enrolled in this echocardiographic follow-up study. Cardiovascular complications, including dysarrhythmias (n = 3, 2.7%), overt congestive heart failure (n = 4, 3.6%), progression of mitral regurgitation over one grade (n = 28, 25.0%), newly confirmed chordal rupture (n = 1, 0.9%), and surgical repair (n = 2, 1.8%), were observed in these patients during a follow-up period of 1–13 years (mean, 4.0 ± 2.8 years). Multivariate analysis and Kaplan-Meier analysis revealed that posterior leaflet prolapse and significant mitral regurgitation (grade ≥2) were considerable risks for cardiovascular complications. Regression of MVP was seen in 17 (18.7%) of the anterior prolapse patients; however, new prolapse was observed in 40 (35.7%) patients, mainly in posterior prolapse patients. These results suggest that site-related differences exist in uncomplicated MVP prognosis and that MVP in the posterior leaflet has a poor outcome compared to that in the anterior leaflet.