Clostridium difficile can cause neonatal enteritis, but has been isolated from both diseased and healthy pigs. C. difficile shedding by pigs is a potential source of zoonotic transmission to humans. The objectives of this study were to characterize the prevalence and genotype of C. difficile with respect to age and health status in the pig industry for the first time in Korea. Fecal samples of 910 pigs were analyzed for the presence of C. difficile. In total, 176 (19.3%) C. difficile strains were isolated. The prevalence was significantly higher (p < 0.01) in diarrheic samples (30.4%) than in non-diarrheic samples (13.3%). The prevalence was highest in diarrheic suckling piglets (53.6%), followed by diarrheic sows (40.0%) and non-diarrheic suckling piglets (34.0%). The toxin genes tcdA, tcdB, cdtA, and cdtB were all detected in 153 isolates (A+B+CDT+, 86.9%). Furthermore, the majority of toxigenic strains (86.5%) were identified as PCR ribotype 078, which is an important pathogen in both pigs and humans. These results indicated that C. difficile is a leading causative pathogen of neonatal diarrhea in piglets in Korea.