ABSTRACT:The pathogenicity of bacterial strains isolated from pathological processes and lesions of horses, strategies for their treatment and the choice of appropriate antimicrobials are frequently a challenging problem for private veterinarians who seek help in our laboratory. Therefore, the aim of this study was to map genera and species of Gram-negative aerobic and microaerophilic microorganisms isolated from pathological processes in horses and to identify the most effective antimicrobial agents for therapy based on antibiotic susceptibility. Between 2009 and 2014 a total of 449 clinical samples (n = 449) were examined; 229 (51%) of them were obtained from the respiratory tract, 121 (27%) from the skin, 40 (8.9%) from the digestive tract, 40 (8.9%) from the eyes, eight (1.8%) from the urinary system, six (1.3%) from the musculoskeletal system, four (0.9%) from the lymphatic system and one (0.2%) from milk. The examination was performed using conventional microbiological culture methods. The identification of isolates was confirmed using MALDI-TOF molecular phenotyping (Bruker Daltonics GmbH, Bremen, Germany). From the 276 Gram-negative isolates (prevalence of 61.5%), the most frequently detected strains were Enterobacter spp., Escherichia spp., Acinetobacter spp., Pseudomonas spp. and Actinobacillus spp. with prevalence rates of 7.6%, 6.7%, 6.7%, 6.0% and 5.8%. In addition, another 20 genera of microorganisms were detected. Susceptibility to antimicrobial agents was determined using the disc diffusion method. The most effective agents were gentamicin (94.1%), enrofloxacin (91.7%), colistin (87.0%), florfenicol (86.2%), neomycin (85.5%), streptomycin (82.4%) and tetracycline (78.5%). A good knowledge of the spectrum of bacterial species participating in pathological processes and lesions in horses and their antimicrobial susceptibility may be of great importance not only in treatment but also in deciding which prophylactic antibiotics to administer after surgical interventions.