Loss of canopy biomass and of annual increment in stem by thinning of different kinds and intensities was computed using the amount of crown biomass and increment of stem of a small number of sample trees and frequency distribution of diameter of stands as basic data. The loss was compared between 13-year-old stands of Cryptomeria japonica of different planting materials: rooted cuttings possibly being a clone and seedlings. In low thinning, the percentage loss was roughly proportionate to the intensity of thinning by basal area, but it was always smaller than the intensity of thinning by number of trees. The deviations of the percentage loss from the intensities of thinning by number of trees was much larger in the stand of seedling origin than in the stand of cutting origin, reflecting the difference in genetic variations among trees. A 17-year-old plantation of Metasequoia glyptostroboides, which is a mixture of two clones, was similar to the stand of seedling origin in these respects. Two types of thinning for the purpose to utilize trees of a certain diameter range were also simulated. The method of estimation of loss of canopy biomass by thinning may be of use for other kinds of partial cutting. Aboveground biomass of the two types of stand of Cryptomeria is presented.