Microbiomic methods are increasingly used to investigate microbial communities in the upper and lower airways. The lungs are no longer considered to be sterile, but instead are understood to contain a diverse microbiota made up of bacteria derived from the upper airways. Much research is now focused on understanding how the respiratory microbiota may contribute to the pathogenesis, treatment response and persistence of upper and lower airway infections. Microbiota research is also driving the development of novel therapies with the potential to alter airway bacterial communities and promote respiratory health (e.g. prebiotics and probiotics). Understanding whether such therapies may be effective across broad populations and different disease contexts requires consideration of the generalisability of respiratory microbiota data. The aim of this presentation is to review key elements of respiratory microbiota studies that may affect generalisability, including potential differences among populations, disease contexts, specimen types and microbiomic methods.