Cover crops are grown to protect and improve soil during fallow periods between crops. The benefits of cover crops include preventing soil erosion, increasing nutrient retention, and suppressing weeds. A challenge associated with cereal rye cover crops is that sometimes there is a decrease in corn yield the following year. Cereal rye is one of the main cover crops planted in Iowa, and like corn is also a grass species. Because of this relationship both grasses may be attacked by the same plant pathogens. I hypothesized that if a winter rye cover crop was terminated with glyphosate a few days before planting corn, then there would be an increase in corn root seedling infection caused by higher levels of pathogens passed on from the dying rye plants. I found that terminating rye cover crops three days before planting corn resulted in an increase in mesocotyl infection and shorter radicles than terminating fourteen days before planting. To evaluate the source of root infection, DNA extractions were conducted to detect specific fungal pathogens in the Pythium and Fusarium genera infecting the corn radical, both three days and fourteen days after termination, with and without using the herbicide glyphosate for termination.