Staphylococcus aureus is a frequent cause of microbial keratitis (MK), conjunctivitis and non-infectious contact lens related corneal infiltrative events (niCIEs). The aim of this study was to determine the rates of resistance of S. aureus isolates from different ocular conditions to commonly used antibiotics and niCIE strains to multi-purpose disinfecting solutions (MPDS). The minimum inhibitory (MIC) and minimum bactericidal concentrations (MBC) was used for susceptibility testing. 51 S. aureus strains from the USA and Australia were evaluated; 14 from niCIEs, 26 from conjunctivitis and 11 from microbial keratitis. 84% of the strains in this study were multi-drug resistant however all strains were susceptible to vancomycin (100%). All the MK strains from Australia were susceptible to ciprofloxacin and oxacillin, whereas only 11% of the MK strains from the USA were susceptible to these antibiotics (p = 0.107). Chloramphenicol susceptibility varied with the ocular condition in USA strains – 96% of conjunctivitis and 55% of MK strains were susceptible to this antibiotic (p = 0.0036). The MPDS OPTI-FREE PureMoist was the most active and Biotrue was least effective against the niCIE strains (p = 0.0231). Knowledge of the rates of resistance to antibiotics could help guide treatment of these diseases.