The pathogens causing pneumonia are difficult to identify because a high quality specimen from the lower lung is difficult to obtain. A new specimen collection device is designed to collect aerosol specimens selectively from the lower lung generated during deep coughing. The PneumoniaCheck device utilizes a separation reservoir and Venturi valve to segregate contents from the upper and lower airways. The device also includes several specially designed features to exclude oral contaminants from the sample and a filter to collect the aerosolized pathogens. Verification testing of PneumoniaCheck demonstrates effective separation of upper airway gas from the lower airway gas and exclusion of both liquid and viscous oral material from the collection chamber. The filters can collect 99.9997% of virus and bacteria sized particles from the sampled lower lung aerosols. The selective collection of specimens from the lower airway may aid in the diagnosis of specific pathogens causing pneumonia.