Liver, fat (adipose tissue), blood, and feces are common endpoints used to determine the bioavailability of persistent organic pollutants (POPs). However, it is not known whether the bioavailability of each endpoints is comparable or whether there is a comprehensive endpoint that can be used for all congeners for the measurement of bioavailability. In this study, we observed the accumulation and distribution of 10 polychlorinated dibenzo-p-dioxins/furans (PCDD/Fs) and 18 polychlorinated biphenyls (PCBs) in different organs of Sprague–Dawley (SD) rats and calculated the bioavailability based on feces, liver, and fat endpoints. Our results indicated that PCB 126, PCB 169, and 50% of PCDD/F congeners were mainly accumulated in the liver, with a bioavailability ranging from 28.9 to 50.6%. On the other hand, higher chlorinated (> 5 Cl) PCB congeners were mainly accumulated in adipose tissues, with a bioavailability ranging from 20.1 to 82.2%, while lower chlorinated (< 5 Cl) pollutants, such as 2,3,7,8-TeCDF, 2,3,7,8-TeCDD, 1,2,3,7,8-PeCDF, and PCB 28, 52, 77, 81, were likely metabolized over 36% in rats during the 8-week experimental period. If we considered metabolization (degradation) as a type of bioavailable process, then the fecal endpoint was a feasible option. However, if we considered the selective accumulation behavior of some congeners in different organs/tissues, then there was no single comprehensive endpoint suitable for all congeners. Lastly, female rats showed significantly higher PCDD bioavailability than male rats at low dose level (0.2 ng/100 g b.w./d); however, the difference in PCB bioavailability between female and male rats was not significant.