Influenza virus is transmitted via respiratory expulsions, but detection of infectious virus in such expulsions has been challenging. Here, we describe quantification and genotyping of infectious virus in respiratory particles using a Modular Influenza Sampling Tunnel (MIST). The particles deposit on cell monolayers, enabling culture, quantification, and sequencing of viruses. Concomitantly, water-sensitive paper and fine particle samplers yield respiratory particle counts over a broad size range. Using the MIST, we captured infectious virus from humans experimentally infected with influenza virus on multiple days post-inoculation. The recovered respiratory particles varied in quantity over three orders of magnitude and contained viral genetic variation that was also detected in samples from infected individuals. Expulsion of infectious virus was associated with infectious viral load in saliva and nasopharyngeal swabs and with clinical symptoms. These data reveal the maintenance of viral diversity in expelled aerosols and suggest that heterogeneity among individuals in the magnitude of infectious expulsions may impact forward transmission potential.