Technical Abstract: Background/Question/Methods Forest disturbance caused by windthrow events has obvious impacts on forest structure and composition above-ground; however, changes in soil microbial communities are less obvious. Windthrows causing the formation of multiple forest gaps occurred in 2003 throughout the Allegany Plateau region of northwestern Pennsylvania. Three years post-disturbance, soil samples were collected from nine replicate pairs of forest gaps and adjacent intact forests. The gaps varied in size from 0.1 to 4 ha. Dilution plating was used to determine if the densities of a common fungal saprobe (Mortierella) and a soil-borne pathogen (Pythium) were greater in intact forest than in newly formed gaps. A subset of Pythium isolates were subsequently used in a pathogenicity experiment using a full factorial design testing the effects of isolate, pathogen inoculum density, and host density on disease symptoms. Results/Conclusions Densities of Mortierella and Pythium were greater in soil from intact forest than in adjacent gaps. Pathogenic activity was density-dependent. Variation in microbial communities inside vs. outside the gaps may affect nutrient cycling and the establishment of tree species. Major forest disturbances appear to disrupt microbial populations and affect the pathogenic activity of the soil which may alter recruitment patterns and affect forest succession if tree species differ in their susceptibility to resident pathogens.