Eosinophil-peroxidase (EPX) is a major constituent of the large cytoplasmic granules of both human and mouse eosinophilic leukocytes. Human EPX-deficiency is a rare, autosomal-recessive disorder limited to the eosinophil lineage. Our intent was to explore the impact of EPX gene-deletion on eosinophil content, structure and function. In response to repetitive intranasal challenge with a filtrate of the allergen, Alternaria alternata, we found significantly fewer eosinophils peripherally and in the respiratory tracts of EPX-/- mice compared to wild-type controls; furthermore, both the major population (Gr1-/lo) and the smaller population of Gr1hi eosinophils from EPX-/- mice displayed lower MFIs for Siglec F. Quantitative evaluation of transmission electron micrographs of lung eosinophils confirmed the relative reduction in granule outer matrix volume in cells from the EPX-/- mice, a finding analogous to that observed in human EPX deficiency. Despite the reduced size of the granule matrix, the cytokine content of eosinophils isolated from allergen-challenged EPX-/- and wild-type mice were largely comparable to one another, although the EPX-/- eosinophils contained reduced concentrations of IL-3. Other distinguishing features of lung eosinophils from allergen-challenged EPX-/- mice included a reduced fraction of surface TLR4-positive cells and reduced MFI for NOD1. Interestingly, the EPX gene-deletion had no impact on eosinophil-mediated clearance of gram-negative Hemophilius influenzae from the airways. As such, although no clinical findings have been associated with human EPX-deficiency, our findings suggest that further evaluation for alterations in eosinophil structure and function may be warranted.