To determine effects of topical antimicrobial and antimicrobial-corticosteroid preparations on the ocular flora of horses. animals: 40 horses. One eye was treated 3 times daily for 2 weeks with one of the following ointments: (1) neomycin-bacitracin-polymyxin B, (2) 0.6% prednisolone-0.3% gentamicin, (3) neomycin-polymyxin B-0.05% dexamethasone, or (4) treated (artificial tears) control. Contralateral eyes of treated control eyes served as untreated control eyes. Corneal and conjunctival specimens for bacterial and fungal cultures were collected prior to initiation of treatment, after 1 and 2 weeks of treatment, and 2 weeks after concluding treatment. Changes in culture growth quantity scores of bacterial and fungal species were analyzed. The most common species before treatment were the following: gram-positive bacteria included Streptomyces spp (66%), Staphylococcus spp (46%), Bacillus spp (32%), and Streptococcus spp (32%); gram-negative bacteria included Moraxella spp (28%), Escherichia coli (24%), Acinetobacter spp (18%), and Enterobacter spp (14%); and fungi included Aspergillus nidulans (56%), Cladosporium spp (32%), and Aspergillus fumigatus (22%). In all groups, the percentage of positive bacterial culture results, growth quantity score of gram-positive bacteria, and number of bacterial species isolated decreased at week 1 and increased at week 2, whereas growth quantity score of gram-negative bacteria decreased throughout treatment. Differences were not significant among groups. Fungal growth quantity score decreased during treatment in all groups. Repopulation of bacterial and fungal species occurred. All interventions decreased the number of microorganisms. Repopulation of normal flora occurred during and after treatment.