The objective of this study was to examine the impact of hospitalisation and antimicrobial drug administration on the prevalence of resistance in commensal faecal E. coli of horses. Faecal samples were collected from ten hospitalised horses treated with antimicrobials, ten hospitalised horses not treated with antimicrobials and nine non-hospitalised horses over a consecutive five day period and susceptibility testing was performed on isolated E. coli. Results revealed that hospitalisation alone was associated with increased prevalence of antimicrobial resistance and multidrug resistance in commensal E. coli of horses. Due to the risk of transfer of resistance between commensal and pathogenic bacteria, veterinarians need to be aware of possible resistance in commensal bacteria when treating hospitalised horses.