Wild cottontail rabbits (Sylvilagus spp.), especially young individuals, are one of the most frequent wildlife species presented for rehabilitation at wildlife rehabilitation centers. These species are challenging to rehabilitate, with gastrointestinal (GI) disease being a major cause of morbidity and mortality during the weaning stage. Two organisms, Clostridium spiroforme and Eimeria spp., are frequently associated with GI disease in young domestic rabbits (Oryctolagus cuniculus) and can result in high rates of morbidity and mortality in this species. Here we present evidence that these two pathogens also play an important role in GI disease in young cottontail rabbits (Sylvilagus audubonii, Sylvilagus floridanus, Sylvilagus nuttallii) undergoing rehabilitation.