The possibility of restoring natural broadleaf forests may be decreased by the effects of plantation management, particularly in sites that undergo repeated rotation. We investigated the following two working hypotheses about the effects of repeated plantation of conifers on the natural regeneration of woody saplings in cool-temperate Japanese cedar plantations: (1) that repeated plantation of conifers decreases sapling species richness, and (2) that repeated plantation of conifers changes sapling species compositions. Our result supported the first hypothesis, because species richness was significantly lower in second-rotation plantations than in first-rotation plantations. The second hypothesis was not supported, because no significant or substantial differences in species composition were observed between plantations with different numbers of rotations. However, the abundance of tree (nonshrub) and gravity-dispersed species decreased after the second rotation of large saplings, albeit not those of small saplings, suggesting that response to repeated rotation depended on sapling size. Our results suggest that it is important to consider factors affecting the maintenance of a species in the plantations, such as distance from natural forests and seed sources, to minimize the effects of repeated plantation.