【Objective】To investigate the value of medical exome sequencing in copy number variation detection in genetic diseases. 【Methods】 Here we tested two separated cases. There are no similar symptoms except intelligent disability between the cases. Fragile X syndrome，G-banding，chromosome microarray and medical exome sequencing were sequenced tested for the two cases and their parents. 【Results】We found the copy number variants in both of the patients from the two families，which distributed from 11.4 kb to 13.03 Mb in size. The copy number variants were all verified by other technologies. 【Conclusion】 medical exome sequencing is useful for the detection of copy number variation in genetic diseases，although the value still need more verification.