Mutant-based studies have contributed to the elucidation of gene functions in plants including tomato. In this review, we introduce some outstanding research performed using spontaneous and artificially induced mutants. Tomato (Solanum lycopersicum L.) is a model species in the solanaceae family and research tools and information necessary to perform functional genomics study are being developed worldwide. Saturation mutagenesis is a powerful strategy that enables exploration of gene function on a genome-wide scale. We reviewed conventional mutant resources of tomato, including the ethyl methanesulfonate (EMS)-mutagenized population of the 'M82', which was developed in Israel (Menda et al., 2004). Recently, a miniature cultivar, 'Micro-Tom', has attracted the attention of tomato researchers due to its small size and rapid life cycle, which make it an ideal experimental organism for handling in the laboratory. We are developing a unique mutant resource, 10,000 EMS-mutagenized and gamma-ray-irradiated lines derived from 'Micro-Tom'. Distinct mutant phenotypes, including plant size, leaf shape, and fruit morphology, are described. The status of newly developed tools for using this mutant resource, such as an efficient transformation method and the Targeting Induced Local Lesions In Genomes (TILLING) system, are also summarized.