The most photosynthetically active leaves of rice seedlings were severely damaged when shoots but not roots were chilled (10°C/25°C, respectively), but no such injury was observed when the whole seedling was chilled (10°C/10°C). To elucidate the mechanisms, we compared the photosynthetic characteristics of the seedlings during the dark chilling treatments. Simultaneous analyses of Chl fluorescence and the change in absorbance of P700 showed that electron transport almost disappeared in both PSII and PSI in the 10°C/25°C leaves, whereas the electron transport rate in PSI in the 10°C/10°C leaves was similar to or higher than that in non-chilled control leaves. Light-induced non-photochemical quenching in PSII was inhibited in the 10°C/25°C leaves, occurring at only half the level in the 10°C/10°C leaves, whereas non-light-induced non-photochemical quenching remained high in the 10°C/25°C leaves. The light induction of Chl a fluorescence (OJIP curves) in the 10°C/25°C leaves was similar to that in leaves treated with DCMU. The fluorescence decay after a single turnover saturating flash in the 10°C/25°C leaves was much slower than in the 10°C/10°C leaves. In vivo analyses of the 550-515 nm difference signal indicated decreased formation of a proton gradient across the thylakoid membrane and decreased zeaxanthin formation in the 10°C/25°C leaves. Our results suggest that electron transport was blocked between Q(A) and Q(B) in the dark 10°C/25°C leaves, but without irreversible damage to the components of this system. The consequent light-dependent losses of electron transport, proton gradient formation across the thylakoids and thermal dissipation may therefore be responsible for the visible injury.