In collaboration with Dr. Charles S. Barnes at Children’s Mercy Hospital, we compared the performance characteristics of four different assays for Alternaria allergen in house dust. The purpose of the study was to provide objective data for deciding which assay to use for the measurement of Alternaria in the National Health and Nutrition Examination Survey 2005-2006. In the National Survey of Lead and Allergens in Housing, we used an assay based on polyclonal antibodies to whole Alternaria extract. Since that survey, an assay based on a monoclonal antibody to the Alternaria allergen Alt a 1 became commercially available. We concluded that using polyclonal antibodies directed against a large range of Alternaria proteins produce the most reliable estimation of overall Alternaria exposure in house dust collections. Based on this data, the laboratory assaying samples for NHANES 2005-2006 will use the polyclonal antibody assay developed against whole Alternaria extract.