Fungal pathogens are thought to be an important source of seed mortality, but their impacts in natural systems are not well understood. In this study, I investigated the effects of fungal pathogens on seed survival in various habitats. An investigation of pathogen impacts on the seeds of eight tree species revealed that most species were affected by fungal pathogens. Fungal impacts differed between habitats for two of the species and these species were also more vulnerable to attack than their more shade-tolerant congeners. An investigation into the role of rotten logs as refuges from fungal pathogens for Eastern Hemlock (Tsuga canadensis) demonstrated that when fungi were an important source of mortality, logs did provide an escape from fungal attack. Overall, the results of this study provide evidence that fungal pathogens contribute to the structure of plant communities via effects on seeds.