Clostridium difficile infection in swine has most often been described in suckling pigs, where it has been associated with mesocolonic edema and typhlocolitis. This prospective study was designed to assess the correlation between the presence of C. difficile toxins (TCd) in the colon contents of neonatal pigs and a number of parameters, including gross evidence of diarrhea, mesocoloninc edema, typhlitis, and colitis. C. difficile was isolated from 51% (66/129) of large intestines and TCd was detected in the colon contents of 50% (65/129) of the piglets. Fifty-eight percent (38/65) of TCd-positive piglets had normal to pelleted colon and rectal contents, whereas 75% (48/64) of TCd-negative pigs had gross evidence of diarrhea. Clostridium difficile toxin-positive animals were significantly more likely to have normal to pelleted feces. Edema of the mesocolon was observed in 38/65 (59%) of TCd-positive piglets. Because a high number of TCd-positive piglets (41%) lacked edema of the mesocolon and a high number of TCd-negative pigs had mesocolonic edema (51%), a statistically significant association between TCd and mesocolonic edema was not identified. Seventy-five percent (49/65) of TCd-positive piglets had colitis and 47/65 (72%) had typhlitis. The association between TCd and both colitis and typhlitis was statistically significant. Apparently healthy piglets were obtained from 5 separate sites. Because TCd was detected in the colon contents of 23/29 (79%) apparently healthy piglets obtained from 5 separate sites, and 70% of TCd-positive control pigs had colitis, C. difficile may represent an important subclinical issue in neonatal swine.