Objective To evaluate the most common bacterial pathogens associated with septic keratitis in veterinary patients from Switzerland. The second objective was to analyze antibiotic susceptibility test results of the identified bacterial pathogens. The third objective was to evaluate potential breed predispositions to septic keratitis. Procedures Two hundred and fifty-five cultures and antibiotic susceptibility reports from dogs, cats, and horses with septic keratitis that were presented to the University of Zurich Veterinary Medical Teaching Hospital between 2009 and 2013 were reviewed. Odds ratios for the risk of having a septic keratitis were estimated for all dog and cat breeds compared to the general nonbrachycephalic hospital population. Results Ninety-six, 29, and 31 positive cultures were obtained from 89 canine, 28 feline, and 29 equine eyes, respectively. Repeat sampling accounted for the differences in numbers. Negative culture results were obtained in 50, 31, and 18 cases. Staphylococci and streptococci accounted for 66% of the isolates in dogs and 80% of the isolates in cats and horses. Staphylococcus spp. had a higher percentage of fluoroquinolone-resistant isolates compared to previous reports. Brachycephalic breeds had elevated odds ratios for the presence of septic keratitis. Conclusion Identified bacterial pathogens and their prevalence as well as the elevated odds ratios for septic keratitis in brachycephalics are roughly consistent with previous studies. Based on systemic breakpoint data, resistance to commonly used topical antibiotics, including the second-generation fluoroquinolones, was found.