Objective: Prader-Willi syndrome (PWS) with different pathogenesis has different clinical manifestations, prognosis and genetic risks. Pathogenesis of the disease cannot be explained by conventional diagnostic method MS-PCR. This study employed methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) for the diagnosis of PWS in order to explore the role of this method in the diagnosis and assessment of pathogenesis of PWS. Methods: A system antithetical method was employed. Peripheral blood samples were collected from 30 children for MS-PCR. Of the 30 children, 16 were diagnosed with PWS by MS-PCR and the other 14 showed negative MS-PCR. MS-MLPA kit Me028 was used to detect DNA extracted from the 30 samples. Results: The results showed by MS-MLPA and MS-PCR were identical. MS-MLPA demonstrated that 4 cases were maternal uniparental disomy and 12 cases were paternal dfeletion in 15q11-q13 region. Conclusions: MS-MLPA is a reliable method of genetic testing for PWS which can distinguish pathogenesis of PWS.