PURPOSE. To compare the bacterial population of the ocular surface of normal and dry eye subjects using conventional culture and 16S rDNA PCR. METHODS. Ninety-one subjects were classified as normal (n = 57) or dry eye (n = 34) by using tear break-up time, McMonnies survey, goblet cell density, and meibomian gland assessment. Conventional bacterial culture and broad-range 16S rDNA PCR, cloning, and DNA sequencing were used for bacterial identification. Repeated sampling was performed in a subset of subjects over a 3-month period. The association between goblet cell loss and bacterial counts in a subgroup of subjects was assessed. RESULTS. Most of the bacteria identified by culture were coagulase negative staphylococci, whereas molecular methods demonstrated a considerable number of additional bacteria. Atypical ocular surface bacteria including Rhodococcus erythropolis, Klebsiella oxytoca, and Erwinia sp., were identified in cases of overt inflammation and, surprisingly, on the normal ocular surface. The same bacteria remained on the ocular surface after repeated sampling. Increased bacterial flora was associated with reduced goblet cell density. CONCLUSIONS. Molecular analysis revealed a diverse ocular surface bacterial population. In addition to the normal flora, various potentially pathogenic bacteria were identified. The detection of known pathogens in both normal and dry eyes, with minimal signs of infection, presents a diagnostic dilemma. It remains unknown whether their presence is associated with inflammation and reduced goblet cell density or whether they adversely affect the ocular surface predisposing it to abnormal microbial colonization. In the absence of overt clinical infection, it is unknown whether such results should prompt intervention with therapy.