To detect the magnitude of indirect positive effects of deer and mice on seedling survival of some woody species in a Japanese temperate forest, we analyzed the data from an earlier field experiment using a hierarchical Bayesian approach. The forest studied was inhabited by sika deer (Cervus nippon) and mice (Apodemus spp.), and the floor was covered with dwarf bamboo, Sasa nipponica, which negatively affected tree seedlings and was in turn negatively affected by deer and mice. The field experiment was designed as the combination of exclusion or removal of these factors: deer, mice and dwarf bamboo. A hierarchical Bayesian model was constructed and the parameters were estimated by the Markov chain Monte Carlo method. The model successfully showed the indirect positive effects of deer and mice, which improved the survival rate of five cohorts of the seedlings of three tree species by ameliorating the direct negative effect of dwarf bamboo. The cohorts studied were formed by the seedlings of Abies homolepis that emerged in 1997 and 2002, those of Fraxinus lanuginosa f. serrata that emerged in 1998 and 2002, and those of Fagus crenata that emerged in 1999. The positive indirect effect was especially large in F. crenata, which is known to be severely affected by dwarf bamboo. The total effect of deer was shown to be positive for all cohorts except the A. homolepis cohort that emerged in 1997, at which time the dwarf bamboo had not yet fully recovered from the browsing pressure of deer. The total effect of mice was shown to be positive for all of the cohorts. We conclude that these positive effects were due to the large negative effect of dwarf bamboo on the seedlings.