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To explore the role of bacteria in the pathogenesis of chronic rhinosinusitis and how the presence of allergies or endoscopic sinus surgery may affect the bacterial flora.As our understanding of the etiologies of chronic rhinosinusitis continues to evolve, the role of bacteria as either a primary or an exacerbating factor remains controversial. It is clear that healthy paranasal sinuses are sterile, but in chronic rhinosinusitis bacteria are often present. It has also been shown that the bacteria found in chronic rhinosinusitis vary significantly from those found in acute rhinosinusitis. In patients with allergic rhinitis an association has been found with higher carriage rates of Staphylococcus aureus. The significance of this is unclear but may be related to bacterial superallergen production leading to TH2-mediated inflammation. Endoscopic sinus surgery does not appear to change the bacterial flora, though it may decrease the presence of bacterial biofilms in sinus cavities.Bacteria are likely to play a role in both the development and the exacerbation of chronic rhinosinusitis. Further studies are needed to determine in which subtypes of chronic rhinosinusitis bacteria play the greatest roles and how our treatments can be individualized to improve patient outcomes.