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Asthma is a common chronic respiratory disease that affects millions of people of all ages in every part of the world. A growing body of epidemiological evidence suggests that early‐life exposure to environment‐derived microbes and farm milk consumption confer protection against allergic disorders. Culture‐independent analyses performed on the human microbiome have provided an overview of microbial communities in various tissue habitats. This chapter provides a synopsis of current knowledge of the airway microbiota and how dysbiosis may underlie the susceptibility to the severity and persistence of asthma and other chronic lung diseases. Sampling of the bronchoal‐veolar space by bronchoalveolar lavage (BAL) remains an important tool for clinical diagnoses as well as experimental models of lung diseases. The development of the airway microbiota in the neonate may be influenced by the: intra …