To describe bacteria isolated from reproductive tracts of mares and to examine the extent and patterns of resistance to antimicrobials commonly used for treatment of endometritis. Retrospective case series. 8,296 uterine swab, lavage, or biopsy samples obtained between January 2003 and December 2008 from 7,665 horses in central Florida. Results of bacterial culture and antimicrobial susceptibility testing were obtained for uterine swab, lavage, and biopsy samples collected from mares undergoing a routine breeding examination or examined because of a reproductive disorder. Bacterial organisms were identified by means of standard techniques, and proportions of samples resistant to various antimicrobials were determined. At least 95% of samples (n = 1,451) were collected with uterine swabs. Potentially pathogenic organisms were cultured from 2,576 (31%) samples, with Escherichia coli (n = 729 [29%]) and β-hemolytic Streptococcus equi subsp zooepidemicus (733 [28%]) being most common. Resistance to antimicrobials changed over time for E coli, S equi subsp zooepidemicus, and Enterobacteriaceae isolates. Overall, E coli was most resistant to trimethoprim-sulfonamide and ampicillin and least to amikacin and enrofloxacin. For S equi subsp zooepidemicus, resistance was greatest to oxytetracycline and enrofloxacin and least to ceftiofur and ticarcillin with or without clavulanic acid. Inflammatory response was greater for S equi subsp zooepidemicus. E coli and S equi subsp zooepidemicus were the most common pathogens recovered from uterine samples, with S equi subsp zooepidemicus more commonly associated with inflammation. Antimicrobials most commonly used empirically to treat endometritis are appropriate on the basis of these data. However, as antimicrobial resistance changes over time, susceptibility assays should aid antimicrobial selection.