Mass mortality of fagaceous trees due to wilt disease, which has been spreading throughout Japan since the 1980s, is caused by the ambrosia beetle Platypus quercivorus. Quercus crispula is one of the species most susceptible to the disease. Previous studies have examined this disease in secondary forests, where fagaceous trees are dominant and are considered to be distributed uniformly. We examined whether the uneven distribution of Q. crispula in a natural forest affects the spread of this disease. We determined its distribution using Morisita's index of dispersion (I delta), and then predicted the probability of mortality using a generalized linear model with topographic variables (altitude and index of convexity), tree size (diameter at breast height, DBH), and basal areas of Q. crispula and Cryptomeria japonica (the dominant species at the study site) per 0.01, 0.09, and 0.25 ha as explanatory variables. The site included 310 Q. crispula within a 14 ha plot in a cool-temperate forest of Japan with no signs of beetle infestation in 2003. The calculated index of dispersion showed a clumped distribution of Q. crispula with an estimated clump size of 0.08 ha. At the end of 2007, 36 Q. crispula in the study site were dead, and DBH and basal area of Q. crispula per 0.09 ha had significant positive effects on the probability of mortality. The basal area of C. japonica, a non-host conifer species for P. quercivorus, per 0.09 ha also had a positive effect on the probability of mortality. These results suggest that P. quercivorus first flew to a cluster of Q. crispula aggregated in about a 0.1 ha area where the density of C. japonica is high, and then DBH played a role in determining the target trees.