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The last few decades have seen an increase in intensive buffalo farms worldwide. Such industrialized activity entails human and animal potential health-related hazards as well as for the environment. Given the breadth of the issue, in this study we focused on gathering microbiological air sampling in the Southern Italian buffalo farms in order to obtain further information on airborne microbial flora. In details, we evaluated the bio-aerosol concentration of cultivable bacteria and fungi in ten different buffalo farms. There are evidences showing that exposure to organic dust may exacerbate asthma, just as it may cause mucous membrane irritation and chronic bronchitis. Likewise, studies show that inhaling noninfectious microorganisms and their components may cause inflammation of the respiratory tract. As a result, this is a significant health hazard to these farms’ workers as well as to rural residents living closely to them.