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The incidence of allergic airway diseases continues to increase in industrial countries while remaining much more stable in developing countries. Allergens inhaled are eventually also swallowed and evidently the gastrointestinal immune system has a role in regulating allergic responses in the pulmonary as well as the GI system. While some studies have pointed out the role of probiotic bacteria as a supplementary protection against the early development of various allergies, little attention has been paid to the composition of the airborne microflora first and continuosly inhaled by newborns and infants. This study compares the composition of two airborne microbial communities, one from hospital delivery rooms and the other from a nature reserve, evidently in use as a birthing place as early as 7500 B.C. around the air from the outdoor birthing place was marked by a far greater variation in microbial composition and a much higher representation of fungi than the air from the hospitals. The dominant bacterial species from the delivery rooms were Staphylococcus areus and Micrococcus luteus, originating from the staff and the hospital environment; the outdoor flora, however, was dominated by Pseudomonas spp. and Bacillus spp. In addition, 56% of all the bacterial isolates from the delivery rooms were most closely related to strains previously associated with clinical infections, whereas only 15% of isolates in the outdoor bacterial sample had such relationships. The role of airborne microorganisms could be important to infants with developing immune systems considering the microbial bias of hospital air presented in this study.