Efficient mutant production systems, through either physical or chemical mutagenesis, have been well established in soybean. A vast amount of genetic variability, of both quantitative and qualitative traits, has been generated through experimental mutagenesis in the past 30 years. Characterization of mutated traits has greatly advanced our understanding of the underlying mechanisms of a score of important traits, including the genetic and genomic basis of nodulation and synthesis of fatty acids and storage proteins. Mutation techniques have also been successfully used in breeding new soybean varieties. More than 100 mutant varieties were developed and released for commercial cultivation; among them are several groundbreaking varieties; i.e., the supernodulating variety Sakukei 4; the glycinin-rich variety Yumenori; the lipoxygenases-free variety Ichihime; and the low linolenic varieties IA3017 and IA2064. It is expected that more new varieties with novel traits will become available in the coming years, and a variety with a reduced phytate level may become available in the near future. Induced mutants will become a unique genetic resource in functional genomic studies, and the advance of functional genomics will increase the usefulness and use efficiency of induced mutations in soybean breeding.