This study evaluated bacterial isolates obtained during abdominal surgery and their relationship to short-term incisional complications. Samples of peritoneal fluid and from resection and/or enterotomy sites from 49 horses were cultured, with 96% having at least one positive culture result. The most common isolates were Escherichia coli, Streptococcus spp, and Enterococcus spp. Horses with small intestinal resections were more likely to grow obligate anaerobes and enteric organisms. Horses with small intestinal lesions (+/- resection) were more likely to grow enteric organisms and less likely to grow non-enteric organisms. Horses without enterotomy or resection procedures were more likely to grow 3 isolates and did not grow obligate anaerobes. The continued incisional drainage rate was 10%. Horses with preoperative peripheral leukocyte counts >8,500 cells/ul were more likely to develop incisional drainage. Many horses undergoing abdominal surgery may have positive intraoperative culture results. Our results did not provide evidence for the routine use of intraoperative culture to predict short-term incisional complications. Further studies are needed to evaluate the value of intraoperative culture in horses at high risk for incisional complications.