Cover crops can offer erosion protection as well as soil and environmental quality benefits. Cereal rye (Secale cereale L.) is the most commonly used winter cover crop in corn–soybean rotations in the upper Midwest of the USA because of its superior winter hardiness and growth at cool temperatures. Cereal rye cover crops, however, can occasionally have negative impacts on the yield of a following corn crop, which discourages broader adoption and introduces substantial risk for corn farmers employing cover crops. We hypothesized that because cereal rye shares some pathogens with corn, it may be causing increased disease in corn seedlings planted soon after cereal rye termination. To test this, we performed a series of experiments in a controlled environment chamber to assess the response of corn seedlings with and without a commercial fungicide seed treatment to the presence of cereal rye or other species of cover crops that were terminated with herbicide prior to corn planting. Our results indicate that under cool and wet conditions, cereal rye reduces corn seedling growth performance and increases incidence of corn seedling root disease. Fungicide seed treatment had limited efficacy in preventing these effects, perhaps because environmental conditions were set to be very conducive for disease development. However, hairy vetch (Vicia villosa Roth) and winter canola (Brassica napus L.) cover crops had fewer negative impacts on corn seedlings compared with cereal rye. Thus, to expand the practice of cover cropping before corn, it should become a research priority to develop alternative management practices to reduce the risk of corn seedling root infection following cereal rye cover crops. Over the longer term, testing, selection and breeding efforts should identify potential cover crop species or genotypes that are able to match the winter hardiness, growth at cool temperatures and the conservation and environmental quality benefits of cereal rye, while avoiding the potential for negative impacts on corn seedlings when environmental conditions are suitable for disease development.