Background Recommendations for antimicrobial prophylaxis for surgery are well-described in human medicine, but information is limited for veterinary practice. Objective To characterize antimicrobial use in horses undergoing emergency colic surgery. Animals A total of 761 horses undergoing emergency colic surgery (20012007). Methods Retrospective case review. Antimicrobial dose and timing, surgical description, and duration of treatment were collected from medical records. Associations between antimicrobial use and the occurrence of fever, incisional inflammation or infection, catheter-associated complications, or Salmonella shedding during hospitalization were analyzed using rank-sum methods and logistic regression. Results A total of 511 (67.2%) horses received an inappropriate amount of drug preoperatively. Median time from preoperative dose to incision was 70 (IQR 5590) minutes; median total surgery time was 110 (IQR 80160) minutes. Seventy-three horses were euthanized under anesthesia because of poor prognosis. Of 688 horses, 438 should have been redosed intraoperatively based on the duration of surgery. Only 8 (1.8%) horses were redosed correctly. Horses remained on perioperative antimicrobials a median of 3 (IQR 24.5) days. Antimicrobial therapy was reinstituted in 193 (28.9%) horses, and median days of total treatment were 3.8 (IQR 26). Signs that led to reinstituting therapy were fever (OR 3.13, P = .001) and incisional inflammation/infection (OR 2.95, P = .001). Horses in which treatment was reinstituted had 2.3 greater odds of shedding Salmonella (P = .003). Increased surgical time was associated with longer duration of antimicrobial therapy (OR 1.02, P = .001). Conclusions and Clinical Relevance Despite published recommendations regarding antimicrobial prophylaxis, compliance is poor; improvement might reduce postoperative complications.