BackgroundProphylactic perioperative antimicrobial protocols in equine synovial endoscopy have been described but not compared with respect to post‐operative outcomes and complications. Increasing antimicrobial resistance in equine practice and interest in promoting judicious use of antimicrobials has prompted reevaluation of drug selection and dosing strategies.ObjectivesTo determine the frequency of and compare post‐operative complications following elective synovial endoscopy between horses receiving different perioperative antimicrobial protocols.MethodsRecords from the Colorado State University Veterinary Teaching Hospital were evaluated (2014–2018) and equine patients undergoing elective synovial endoscopy were identified. Patients undergoing endoscopy for sepsis or internal fixation were excluded. Patient signalment, clinician, joint and limb involved, perioperative antimicrobial regimen, number endoscopic portals and closure technique, and post‐operative complications including incidence of joint infection were recorded. Generalized linear models were used to estimate the odds of post‐operative complications.ResultsElective synovial endoscopies of 516 horses in 537 procedures evaluating 761 synovial structures were performed. No horses developed post‐operative septic synovitis. Administration of post‐operative antimicrobials, type used and patient sex were all significantly associated with increased risk of complications, which were predominantly gastrointestinal‐related. Complication rates in horses receiving a single preoperative dose of cefazolin were lower than in horses receiving potassium penicillin, gentamicin or multiple doses. Complication rates were lower in females compared to castrated or intact males. Other factors evaluated (breed, age, surgeon, anaesthesia duration or hospitalization, joint/limb operated, number endoscopic portals) were not associated with increased risk of complications post‐operatively in this case population.ConclusionsProphylactic perioperative antimicrobial protocols in equine practice deserve periodic reconsideration due to increased antimicrobial resistance. Prolonged antimicrobial usage beyond the time of surgery was unnecessary to prevent septic synovitis following synovial endoscopy in this case population and was furthermore associated with an increased risk of gastrointestinal complications.