In order to elucidate ultimate biological function of the genome, the model animal system carrying mutations is indispensable. Recently, large-scale mutagenesis projects have been launched in various species. Especially, the mouse is considered to be an ideal model to human because it is a mammalian species accompanied with well-established genetic as well as embryonic technologies. In 1990's, large-scale mouse mutagenesis projects firstly initiated with a potent chemical mutagen, N-ethyl-N-nitrosourea (ENU) by the phenotype-driven approach or forward genetics. The knockout mouse mutagenesis projects with trapping/conditional mutagenesis have then followed as Phase II since 2006 by the gene-driven approach or reverse genetics. Recently, the next-generation gene targeting system has also become available to the research community, which allows us to establish and analyze mutant mice carrying an allelic series of base substitutions in target genes as another reverse genetics. Overall trends in the large-scale mouse mutagenesis will be reviewed in this article particularly focusing on the new advancement of the next-generation gene targeting system. The drastic expansion of the mutant mouse resources altogether will enhance the systematic understanding of the life. The construction of the mutant mouse resources developed by the forward and reverse genetic mutagenesis is just the beginning of the annotation of mammalian genome. They provide basic infrastructure to understand the molecular mechanism of the gene and genome and will contribute to not only basic researches but also applied sciences such as human disease modelling, genomic medicine and personalized medicine.