Whole exome sequencing (WES) with next-generation sequencing (NGS) is a powerful and cost-effective method for detection of mutations and small indels in all exons. The application of WES has been widened to analyses of somatic mutations. However, polymerase chain reaction (PCR) error during library preparation is the most resistant obstacle for detection of de novo, low-frequency mutations. In this study, we succeeded the development of a PCR-free WES method. Using this method, 2 µg DNA was sufficient for library preparation for whole exome sequencing. Furthermore, the method is simple and makes use of a commercial kit, with additional step of concentrating the captured library by ethanol precipitation. The accuracy of the PCR-free method was found to be equivalent to that of unique molecular identifier-corrected analysis method, which is the commonly used method to detect rare mutations. Thus, the PCR-free whole exome sequencing method is cost-effective as well as efficient in detecting rare mutations.