The main sources of dioxin emissions are municipal solid waste incinerators. The Japanese national government has set an emission standard for dioxins to reduce dioxin exposure levels. In this study, cost-effectiveness analyses are carried out regarding countermeasures that were recently taken and are being taken at municipal solid waste incinerators in Japan. Annual costs were estimated by telephone survey and model calculations. Annual decrease in the incidence of cancer was estimated in three steps. First, the annual decrease in the volume of dioxin emissions was estimated. Next, using a mathematical model, the annual decrease in human exposure was estimated. Finally, the annual decrease in the incidence of cancer was estimated by applying the cancer slope factor. When annual costs are divided by the annual number of life-years saved, cost per life-year saved (CPLYS) was obtained. CPLYS was estimated to be 7.9 million yen for emergency countermeasures and 150 million yen for long-term countermeasures. However, it must be noted that these obtained CPLYSs are highly dependent on the cancer slope factor and should be considered as an upper limit since there may be a cancer effect threshold.