The incidence of chronic kidney disease and its progression to end-stage renal disease (ESRD) differs between genders, so it can be surmised that the incidence of ESRD is different between men and women. We analyzed the annual incidence of ESRD by gender for a 20 year period, from 1983 to 2002, using Japanese Society for Dialysis Therapy (JSDT) registration data. The annual incidence of ESRD was calculated as the number of incident dialysis patients divided by the census population of the previous year in each gender, and expressed per million of each population (male and female). In men, the incidence of ESRD increased from 99.9 in 1983 to 330.2 in 2002, whereas it was 66.6 in 1983 and 184.9 in 2002 in women. The difference of incidence of ESRD from men to women increased from 33.3 in 1983 to 145.3 in 2002. The mean age at the start of dialysis was 51.5 years (men) and 52.5 years (women) in 1983, it increased to 63.8 years (men) and 66.1 years (women) in 2002. The difference in mean age increased from 0.9 years in 1983 to 2.3 years in 2002. There was no clear relationship between the available dialysis station per 100,000 population and the men to women ratio in the prevalent dialysis patients among the 47 prefectures. The acceptance of dialysis therapy might not be strong enough to explain the increasing difference in ESRD incidence between men and women in Japan. Differences in the socioeconomic conditions and lifestyles between men and women, which might be related to the gender difference in incidence in ESRD, should be studied further.