Abstract Germination and seedling survival of some woody plants were examined in a colony of the common cormorant at Unoyama, central Japan. The germination of Quercus serrata and Pinus densiflora was less successful in the colony than outside the colony. The percentage of germination success was negatively correlated with the amount of cormorant faeces scattered on the ground and also with the soil water conent. Most of the germinated seedlings inside of the colony died with symptoms such as necrosis spreading from the edge of leaves. Saplings of Q. serrata also tended to die more in the colony than outside the colony. The survival rate of Quercus glauca seedlings with scattered faeces on their leaves and/or on the the surrounding soil was significantly lower than the rate of those free of faeces. These results suggest that in the cormorant colony, germination of seeds and seedling survival are greatly inhibited due to both the direct and indirect effects of cormorant faeces.