There is no specific criteria established to guide physicians in the differential diagnosis of primary mitral valve prolapse (MVP) and rheumatic MVP. Previous studies suggested that history and pathology of mitral valve could be helpful in differential diagnosis of MVP. The aim of this study was to evaluate the value of QT interval, QT dispersion, and diastolic function in differential diagnosis of MVP. We examined electrocardiographies and echocardiographies of 24 primary MVP patients, 20 rheumatic MVP patients, and 21 healthy subjects. MVP was defined as superior displacement of the mitral leaflets more than 2 mm into the left atrium during systole. QT dispersion was significantly higher in primary MVP patients (71 ± 13.5 ms, p < 0.01). Maximum QT dispersion value in rheumatic MVP patients was 55 ms. E and A velocity values which show ventricular early and late diastolic filling, were lower in primary MVP patients (p < 0.01). There was no difference in the heart rate corrected QT interval values between the primary MVP patients (397 ± 28.1), rheumatic MVP patients (403 ± 23.8) and healthy children (404 ± 15.8; p > 0.05). Our findings may indicate that QT dispersion can be used as a parameter for differential diagnosis of primary MVP and rheumatic MVP. Further studies are needed to identify a cut-off point of QT dispersion.