The prefecture of Okinawa is known for the longevity of its population, for 30 years it had the longest life expectancy of all prefectures in Japan. However this advantage was lost in 2000 and male longevity is now ranked 26th among the 47 prefectures of Japan. The aim of this study was to explore whether the recent decline in Okinawan life expectancy advantage is due to the cohort effect of low birthweight infants becoming middle- and older- aged Okinawans. This is an observational study using existing demographic and health statistics. Data on life expectancy, mortality and low birthweight rates were obtained from the Okinawan Prefectural Department of Health and Welfare and the Japanese Ministry of Health, Labour and Welfare. In the year 2000 the longevity advantage of Okinawan males over the Japanese mainland was lost and the relative life expectancy of females declines. The mortality ratio for heart disease has reversed showing a cohort effect, with younger Okinawans having higher death rates than those living in the rest of Japan. The low birthweight rate for Okinawa is 20% greater than mainland Japan. As the post World War cohort of low birthweight infants reaches middle age, the longevity advantage of Okinawans has been lost. The loss of the longevity advantage of Okinawa over the rest of Japan may be due to the increase in non-communicable disease in the post war cohort that has experienced a higher low birthweight rate.