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Background: Most studies of indoor allergens have focused on the home environment. However, schools may be an important site of allergen exposure for children with asthma. We compared school allergen exposure to home exposure in a cohort of children with asthma. Correlations between settled dust and airborne allergen levels in classrooms were examined., Methods: Settled dust and airborne samples from 12 inner-city schools were analyzed for indoor allergens using multiplex array technology (MARIA). School samples were linked to students with asthma enrolled in the School Inner-City Asthma Study (SICAS). Settled dust samples from students' bedrooms were analyzed similarly., Results: From schools, 229 settled dust and 197 airborne samples were obtained. From homes, 118 settled dust samples were obtained. Linear mixed regression models of log-transformed variables showed significantly higher settled dust levels of mouse, cat and dog allergens in schools than homes (545% higher for Mus m 1, estimated absolute difference 0.55 μg/g, p < 0.0001; 198% higher for Fel d 1, estimated absolute difference 0.13 μg/g, p = 0.0033; and 144% higher for Can f 1, estimated absolute difference 0.05 μg/g, p = 0.0008). Airborne and settled dust Mus m 1 levels in classrooms were moderately correlated (r = 0.48; p < 0.0001). There were undetectable to very low levels of cockroach and dust mite allergens in both homes and schools., Conclusion: Mouse allergen levels in schools were substantial. In general, cat and dog allergen levels were low, but detectable, and were higher in schools. Aerosolization of mouse allergen in classrooms may be a significant exposure for students. Further studies are needed to evaluate the effect of indoor allergen exposure in schools on asthma morbidity in students with asthma., (© 2012 John Wiley & Sons A/S.)