This study investigated the differences in bioavailability and tissue accumulation efficiency between all-E- and Z-isomer-rich carotenoids after oral administration to rats. Three commercially important carotenoids (lycopene, β-carotene, and lutein) were chosen for the study. For all carotenoids, feeding with Z-isomer-rich diets increased their concentrations in plasma and tissues at least similar to or more than the all-E-isomer-rich diets, e.g., in rats fed a Z-isomer-rich lycopene, the lycopene concentrations in the plasma and liver after the 2-week administration were respectively 6.2 and 11.6 times higher than those fed an all-E-isomer-rich diet. These results strongly indicate that carotenoid Z-isomers have higher bioavailability and tissue accumulation efficiency than the all-E-isomers. Moreover, diets rich in carotenoid Z-isomers significantly improved the total Z-isomer ratio in plasma and several tissues compared to the all-E-isomers. Since carotenoid Z-isomers potentially have higher antioxidant activity than the all-E-isomers, their accumulation in the body might bring remarkable health benefits.