Exposure to common indoor allergens is known to be associated with sensitization and triggers of asthma. Levels of allergens have been barely described in Mediterranean countries. This study reports domestic allergen levels among the general population of two regions of Spain. Dust samples were collected from living rooms and mattresses in homes of infants in Barcelona (n = 366) and Menorca (n = 475) and assayed for house dust mite (Der p 1) and cat allergen (Fel d 1) concentrations by enzyme-linked immunoabsorbent assay (ELISA). Geometric mean values (95% CI) of Der p 1 were 0.77 µg/g (0.65, 0.92) in living rooms and 0.68 (0.56, 0.82) in children's mattresses in Barcelona, and 9.06 (7.93–10.34) and 3.12 (2.71–3.59) in Menorca, respectively. Fel d 1 levels were 0.37 µg/g (0.31, 0.45) and 0.14 (0.12, 0.18) in Barcelona, and 0.42 (0.35, 0.50) and 0.20 (0.18, 0.24) in Menorca. Home characteristics were not consistently related to levels of aeroallergens in either location. Differences in Der p 1 levels in the two locations indicate that levels cannot be extrapolated from one part of a country to another with any certainty. Additionally, allergen reduction measures related to indoor sources must be specific to each location.