The effects of winter cover crops on root disease and growth of corn and soybeans is poorly understood. A three-year field experiment investigated the effect of winter cereal rye (Secale cereal L.) and winter camelina [Camelina sativa (L.) Crantz] used either in all three years or in rotation with each other, on corn (Zea mays L.) and soybean [Glycine max. (L.) Merr.] growth, root disease, and yield. Corn following a cover crop of camelina had reduced root disease, a lower Pythium population in seedling roots and greater growth and yields compared to corn following a rye cover crop. Camelina and rye cover crops before soybean had either a positive or no effect on soybean growth and development, root disease and yield. Moreover, Pythium Clade B populations were greater in corn seedlings after a rye cover crop compared to those following a camelina cover crop, while Clade F populations were greater on soybean seedlings following a camelina cover crop compared to seedlings following a rye cover crop. Winter camelina cover crop grown before corn had less negative effects on corn seedling growth, root disease, and final yield than a winter rye cover crop before corn. Neither cover crop had negative effects on soybean and the cover crop in the preceding spring had no measurable effects on either corn or soybean.