Microbial flora from the right eye conjunctival sac of 84 consecutively presenting contact lens patients were compared with cultures from both surfaces of their lens after aseptic removal and with the flora of their storage cases. Similar results were obtained from contact lens and conjunctival cultures of each individual; however, there was no correlation between storage case isolates and lens or conjunctival flora, suggesting that in uncomplicated lens wear, the eye is highly efficient in eradicating microorganisms introduced via handling. Conjunctival flora during daily contact lens wear was similar to the conjunctival flora of a matched control group of non-lens wearers. However, bacteria that are considered to be part of the normal ocular flora were isolated significantly more often from former contact lens wearers. The data also indicated that the use of nonperoxide chemical lens disinfection was associated with a higher proportion of positive cultures for pathogenic microorganisms than the use of other forms of disinfection, for both current and former contact lens wearers. The isolation of potential pathogens was particularly common among elderly subjects using thick contact lenses for extended wear. These changes to conjunctival flora may contribute to the increased risk of ocular infection associated with contact lens wear.