Abstract. This survey was undertaken to determine the relative frequency of agents that are currently associated with neonatal diarrhea in swine, including Clostridium difficile and porcine reproductive and respiratory syndrome virus (PRRSV). The subjects for this study were the first 100 live 1-7-day-old piglets submitted to the Iowa State University Veterinary Diagnostic Laboratory with a clinical signalment of diarrhea, beginning on January 1, 2000. The evaluation of each pig included bacterial culture of a section of ileum, 2 sections of jejunum, and a single section of colon; a fluorescent antibody test (FAT) or immunohistochemistry (IHC) for transmissible gastroenteritis virus (TGEV); ELISA's for rotavirus and C. difficile toxins; IHC for PRRSV; and microscopic examination of ileum, midjejunum, spiral colon, liver, spleen, and lung. Survey results demonstrate a decline in the relative number of diagnoses of TGEV, Escherichia coli, and Clostridium perfringens type C compared with retrospective data. The combined case frequency rate for these 3 pathogens dropped from 70% in 1988 to 21% in 2000. This survey also demonstrated the emergence of C. difficile as an important pathogen of neonatal swine. Clostridium difficle toxin was detected in the colon contents of 29% of the piglets, and at least 1 toxin-positive animal was identified in 55% of the cases. All 29 C. difficile toxin-positive piglets had mesocolonic edema, and colitis was observed in 21 of 29 toxin-positive animals. PRRSV-positive macrophages were detected in the lamina propria of intestinal villi by IHC in 10 piglets with diarrhea. In 6 of these cases, PRRSV was the only pathogen detected. Gross and microscopic lung lesions were not a reliable indicator of PRRSV infection in these neonatal pigs with diarrhea. The addition of tests for C. difficile and PRRSV to a routine neonatal diarrhea diagnostic protocol resulted in a significant increase in the diagnostic success rate on both individual animal and case bases.The composition and priority rank of differential diagnoses for common disease syndromes is continuously changing as management practices, emerging diseases, and government programs alter the relative prevalence of contributing agents. This appears to be particularly true of neonatal diarrhea in swine. A report outlining retrospective diagnostic laboratory data from 1988 indicates that Escherichia coli and transmissible gastroenteritis (TGE) were each detected in 26% of suckling pigs with diarrhea, clostridial enteritis in 18%, coccidiosis in 15%, and rotavirus in 8% of the cases. 13 Escherichia coli, TGE, and necrotic clostridial enteritis combined to account for 70% of the case diagnoses in 1988. 13 These 3 diseases were detected in only 26% of neonatal diarrhea cases submitted to the Iowa State University Veterinary Diagnostic Laboratory (ISU VDL) in 1999. Clostridium perfringens type A and Clostridium difficile, 2 diseases that were not reported in the retrospective study from 1998, were identified in 7% of the neonatal diarrhea cases ...