The time it takes seeds to pass through the gut of vertebrates is an important aspect of endozoochorous seed dispersal because it influences seed dispersal distance. The physical characteristics of seeds (e.g. dry seed weight, volume and specific gravity) vary among plant species, which might cause a difference in seed movement through the gastrointestinal system. We conducted feeding experiments with captive female Japanese macaques Macaca fuscata (n=5) using eight different types of seeds to evaluate the effects of the physical characteristics of seeds on their passage time. The median seed recovery percentage for the real seeds was 35.5% (range, 24–78%). Among three passage time variables examined, the mean retention time (MRT) (37–54 h) and time of last appearance of a seed (TLA) (53–109 h) differed significantly among seed types, and the former differed significantly among individuals. Transit time (TT) (22–35 h) did not. The generalized linear models (GLM) selected dry seed weight as the most important factor affecting MRT, and specific gravity of seeds as the most important factor affecting TLA. This implies that (1) heavier seeds and (or) seeds with greater specific gravity remain in the gut longer and are likely to be dispersed farther from the parent plant; (2) the lighter seeds and (or) seeds with lower specific gravity are dispersed nearer the parent. Our study demonstrated the importance of considering the effects of the physical characteristics of seeds on the manner in which primates disperse plant species, although we should consider the effect of the individual variation in the passage time, too.