Root temperature is found to be a very important factor for leaves to alter the response and susceptibility to chilling stress. Severe visible damage was observed in the most active leaves of seedlings of a japonica rice (Oryza sativa cv. Akitakomachi), e.g. the third leaf at the third-leaf stage, after the treatment where only leaves but not roots were chilled (L/H). On the other hand, no visible damage was observed after the treatment where both leaves and roots were chilled simultaneously (L/L). The chilling injury induced by L/H, a novel type of chilling injury, required the light either during or after the chilling in order to develop the visible symptoms such as leaf bleaching and tissue necrosis. Chlorophyll fluorescence parameters measured after various lengths of chilling treatments showed that significant changes were induced before the visible injury. The effective quantum yield and photochemical quenching of PSII dropped dramatically within 24 h in both the presence and absence of a 12 h light period. The maximal quantum yield and non-photochemical quenching of PSII decreased significantly only in the presence of light. On the other hand, L/H chilling did not affect the function of PSI, but caused a significant decrease in the electron availability for PSI. These results suggest that the leaf chilling with high root temperature destroys some component between PSII and PSI without the aid of light, which causes the over-reduction of PSII in the light, and thereby the visible injury is induced only in the light.