To investigate the recent changes in background exposure to dioxin-related compounds, the concentrations of polychlorinated dibenzo-p-dioxins (PCDDs), polychlorinated dibenzofurans (PCDFs), and dioxin-like polychlorinated biphenyls (dl-PCBs) in the blood of individual residents in Japan were repeatedly examined. Twenty-six subjects (mean age, 52.7 +/- 1.8) from District A and 23 subjects (mean age, 56.1 +/- 1.2) from District B were longitudinally analyzed from 2002 to 2006. District A is a rural area in Osaka prefecture, and District B is an urban area in Saitama prefecture. For the longitudinal analysis of these concentrations, we used the generalized estimating equation (GEE). The PCDD + PCDF concentrations decreased significantly between 2002 and 2006 (p < 0.0001), but the concentrations of dl-PCBs declined to a smaller degree over the 5-year period. A time x body mass index (BMI) interaction suggests that the reduction rate of blood PCDDs + PCDFs and dl-PCB concentrations in subjects with a BMI greater than the 75th percentile is lower than that of subjects with a BMI less than the 75th percentile from 2002 to 2004 over the 5-year period. From other reports on the dietary intake of PCDDs, PCDFs, and dl-PCBs in Japan, the total amount of daily dioxin intake decreased, but the percentage of dl-PCBs increased yearly in the first half of the 2000s. The reason for the difference in the 5-year change in blood concentrations between PCDDs +PCDFs and dl-PCBs may be explained by the yearly change in the dietary dioxin intake.