In the largest study to date of bacterial flora in newborns, we cultured the conjunctivae of 100 infants within 15 minutes after vaginal delivery and before any antimicrobial agents had been applied to the eye. All cultures were intensively analyzed for anaerobic and aerobic bacteria. By far the largest group of bacteria isolated were microaerophilic, such as Lactobacillus species and diphtheroids, accounting for 46.8% of positive cultures and 62.3% of all bacteria isolated. The second largest group were true anaerobic bacteria, such as Bacteroides and Propionibacterium species. The smallest group were aerobic bacteria. This incidence of non-aerobic bacteria in the conjunctiva of newborns is the highest reported to date. Our finding should alert clinicians to consider non-aerobic, especially microaerophilic, bacteria in the differential diagnosis of ophthalmia neonatorum. The high rate of supposedly sterile cultures reported in other studies may be explained at least partially by improper isolation of non-aerobic bacteria.