Many studies now suggest that pathogens can cause high levels of mortality in seeds and seedlings. Recruitment from seed to sapling is an important bottleneck for many tree species, and if specialist or generalist pathogens have differential negative effects among species of juvenile trees, then they may have a significant impact on forest community structure. To explore the effects of differential pathogen attack among tropical tree species, we quantified pathogen attack on the seeds of 16 tree species from the southeastern Peruvian Amazon and asked which seed characteristics, including size, hardness, germination time and mode, shade tolerance, and fruit type, were most closely correlated with susceptibility to pathogens. Shade tolerance and seed weight were positively and significantly correlated with susceptibility to pathogen attack by ecological trait regressions (ETRs), and correspondence analysis indicated that there might be increased attack rates in species with brightly colored, pulpy fruits (often dispersed by primates). Only shade tolerance was significantly correlated with pathogen attack when the analyses accounted for phylogenetic relatedness between species. Thus, contrary to standard predictions of size-defense ratios, our results suggest that larger, shade-tolerant seeds tend to be more susceptible to pathogen attack than smaller, light-dependent seeds. Moreover, differential pathogen attack may shape seed community composition, which may affect the successful recruitment of adults. © 2007 Springer Science+Business Media, Inc.