In oncology, next generation sequencing and comprehensive genomic profiling have enabled detailed classification of tumors using molecular biology. It, however, may be unrealistic to conduct phase I-III trials according to each subpopulation based on the molecular subtypes. Common protocols that assess the combination of several molecular markers and their targeted therapies by means of multiple sub-trials are required. These protocols are called “master protocols,” and are drawing attention as a next-generation clinical trial design. In this review, we provide an overview of clinical trials based on master protocol including basket, umbrella, and platform trials along with their recent examples. We also discuss the statistical challenges encountered in their application.