Ciprofloxacin 0.3% ophthalmic solution has been shown to be effective in the treatment of bacterial keratitis and conjunctivitis, and many physicians use ciprofloxacin as sole therapy in these conditions. In this retrospective study, we found seven of 84 isolates from corneal and conjunctival cultures that were resistant to ciprofloxacin. All of the resistant organisms were gram positive. Six of the isolates (Staphylococcus aureus, Staphylococcus hominis, and four isolates of the Streptococcus viridans group) were from corneal cultures, and one (Staphylococcus aureus) was from a conjunctival culture. Yearly records of systemic isolates from 1988 to 1993 (n = 35,308) demonstrated a statistically significant decrease in susceptibility for several organisms that are common pathogens in the conjunctiva and cornea: Pseudomonas aeruginosa (95-90%, p = 0.001); Staphylococcus aureus (96-87%, p < 0.0001); Staphylococcus spp., coagulase negative (97-81%, p < 0.0001); Enterococcus spp. (92-79%, p < 0.0001); Acinetobacter anitratus (97-77%, p = 0.0006); and Enterobacter cloacae (100-96%, p = 0.03). Although the susceptibility of corneal and conjunctival isolates in this series remained relatively high (91.7%), a much larger series of systemic isolates that are common ocular pathogens revealed a statistically significant increase in resistance to ciprofloxacin over the preceding 5 years.