Cockroach, dust mite, cat, dog, mouse, and molds are major indoor allergens that have been associated with the development of allergic diseases and disease morbidity in allergen-sensitized individuals. Physical characteristics, such as allergen particle size, hydrophobicity, and charge, can determine an allergen’s propensity to become airborne, location of respiratory tract penetration, and ability to elicit IgE responses in genetically predisposed individuals. Standardization and recent advancements in indoor allergen assessment serve to identify sources and distribution of allergens in a patient’s home and public environment, inform public policy, and monitor the efficacy of allergen avoidance and therapeutics.