Allergic asthma and influenza are both diseases of the pulmonary system that affect millions worldwide. During the 2009 influenza pandemic, asthma was identified as an underlying disease in hospitalized patients, although reasons for this increased susceptibility were unknown. Animal models are necessary to explore mechanisms of disease pathogenesis. However, models that could be used to study influenza virus infections in existing asthma are lacking. This protocol describes the development of mouse model systems of asthma and influenza comorbidity using an Aspergillus fumigatus-induced asthma model and the 2009 pandemic H1N1 influenza strain A/CA/04/2009. The host responses that occur in acute and chronic asthma can be explored by changing the timing of the influenza virus infection. These models suggest that the allergic host response to influenza virus depends on the state of the allergic airways and level of allergic inflammation.