To investigate the radiocarbon concentration of atmospheric CO2 over the past few millennia in Japan, we measured the 14C age of annual rings from 3 Japanese trees with calendar dates ranging from ∼2000 yr old to present, and we compared the tree-ring 14C age with the corresponding 14C age from IntCal09. In some instances, the 14C ages of the annual rings of Japanese trees are not consistent with the IntCal09 data sets. Often, the 14C ages of tree rings are older than those from IntCal09, but younger than those from the SHCal04 data sets. The average shifts in the Nagoya 14C age from IntCal09 data sets and 1σ errors were determined to be +26 ± 36, +24 ± 30, +16 ± 22, +5 ± 21, and +14 ± 22 14C yr for the intervals AD 72– 382, 589–1072, 1413–1615, 1617–1739, and 1790–1860, respectively. The Japanese Archipelago is situated near the boundary of the Intertropical Convergence Zone in summer, and the 14C concentration of atmospheric CO2 over Japan can be influenced by air masses of the Southern Hemisphere with lower 14C concentrations during periods of higher solar activity and heightened East Asian summer monsoons. Our results suggest that the Japanese Archipelago is located in a critical zone where it is difficult to calibrate the 14C age of tree-ring samples using existing calibration data sets. It should be noted that calibration of the 14C dates of Japanese samples with IntCal09 may induce additional systematic shifts of calibrated ages toward older ages by about 30 yr compared with the sample optimum calendar ages.