Airborne mouse allergen is a risk factor for respiratory diseases. Conventional assessment techniques provide mass-based exposure estimates that may not capture completely the inhalation risk of airborne allergen particles. In contrast to mass-based estimates, the halogen immunoassay (HIA) combines immunoblotting and microscopy to directly assess allergen-containing particles. We evaluated the HIA for the assessment of airborne mouse allergen and compared the results to the enzyme linked immunosorbent assay (ELISA). Particulate matter (PM)10 and PM2.5 samples (30 min, 4 l/m) were collected in a mouse facility before, during, and after disturbance of soiled bedding. Concentrations of Mus m 1-positive particles (haloed particles (HPs)) and intensities of the haloes were determined with the HIA. Although HPs/m3 were positively correlated with mass concentration (statistically significant only with Mus m 1 concentration on PM10), replicates of mass concentration showed higher variability than HPs/m3. After disturbance, most of the HPs were in the PM2.5 fraction. Mean haloes intensities were similar before, during, and after disturbance. The HIA was able to measure allergen-containing particles with less variability than the ELISA, detected the shift of HPs to smaller particles after disturbance, and may suggests similar halo intensity by particles detected during and after disturbance. Our findings suggest that the HIA can be used to assess indoor concentrations of mouse allergen particles and their morphological characteristics.