Shoots grafted into the upper crowns of tall Japanese cedar (Cryptomeria japonica D. Don) show foliar gas exchange characteristics similar to those of intact shoots Abstract The lower foliar photosynthetic rates seen in shoots in the upper crowns of tall trees than those in seedlings could be caused by extrinsic factors, such as hydraulic conductance, for shoots or by irreversible intrinsic change in the meristems during tree development. To clarify which is most significant, we compared foliar gas exchange characteristics and water relations among scions of Japanese cedar (Cryptomeria japonica D. Don) grafted into the upper crowns of tall trees, rooted cuttings developed from scions of the same clones, and intact shoots in the upper crowns of the tall trees. Grafted shoots had the same water regime as intact shoots, as confirmed by their similar water potentials at the turgor loss point, which were more negative than those of the rooted cuttings. No significant difference was observed between the grafted and intact shoots in their light-saturated photosynthetic rate (P max ), stomatal conductance (g s ), photosynthetic capacity, carboxylation efficiency, ratio of intercellular to ambient CO 2 concentration (C i /C a ), and carbon isotope composition (δ 13 C). Compared with the rooted cuttings, the grafted shoots showed significantly lower P max , g s , photosynthetic capacity, and carboxylation efficiency (to 49%, 31%, 68%, and 65%, respectively). The C i /C a and δ 13 C indicated significantly stronger instantaneous and long-term stomatal limitation in the grafted shoots than in the rooted cuttings. These indicate that changes in extrinsic factors can reduce foliar photosynthetic rates in shoots in the upper crowns of tall trees as a result of stronger stomatal limitation and reduced photosynthetic activity, without irreversible intrinsic changes in the meristems.