INTRODUCTION Ocular surface disorders and infections in sulfur mustard (SM) exposed patients are of particular clinical importance. The aim of the present study is to detect the conjunctival bacterial florae in patients with seriously SM induced eye injuries. MATERIALS AND METHODS Conjunctival bacterial florae of 143 seriously eye injured subjects as the study group was detected. The results were compared with 26 normal participants. Both groups were matched in age and sex. The samples were taken by sterile swab from interior fornixes of conjunctiva in both groups and were transported to microbiology laboratory by Stuart's Transport Medium. All samples were inoculated onto Blood agar, Mac Conkey agar and Chocolate agar and isolated microorganisms were identified by biochemical tests. The data were analyzed by SPSS and Man Whitney tests. RESULTS Nineteen cases (13.39%) and none of the controls (0%) had positive culture results (p = .043). Isolated microorganisms from patients included coagulase-negative staphylococci 10 cases (52.6%), Staphylococcus aureus 5 cases (26.3%), non enterobacteriaceae gram negative bacilli 2 cases (10.5%), Penicillium spp. 2 cases (10.5%), Citrobacter sp. 1 case (5.2%), non-spore forming Gram positive bacillus 1 case (5.2%) and α hemolytic streptococcus 1 case (5.2%). Two patients had mixed microorganisms and other patients had just one microorganism. Most of the S. aureus isolates were sensitive to usual antibiotics. CONCLUSIONS The results of this study showed that the prevalence rate of conjunctival bacterial isolates in patients with seriously SM induced ocular injuries are higher and potentially more dangerous than normal controls.