Previous studies report associations between aeroallergen exposure and asthma exacerbations. Aeroallergen burdens and asthma prevalence are increasing worldwide and are projected to increase further with climate change, highlighting the importance of understanding population-level relationships between ambient pollen concentrations and asthma. We sought to examine short-term associations between ambient concentrations of various pollen taxa and emergency department (ED) visits for asthma and wheeze in the Atlanta metropolitan area between 1993 and 2004. We assessed associations between the 3-day moving average (lag 0-1-2) of Betulaceae (except Alnus species), Cupressaceae, Quercus species, Pinaceae (except Tsuga species), Poaceae, and Ambrosia species pollen concentrations and daily asthma and wheeze ED visit counts, controlling for covarying pollen taxa and ambient pollutant concentrations. We observed a 2% to 3% increase in asthma- and wheeze-related ED visits per SD increase in Quercus species and Poaceae pollen and a 10% to 15% increased risk on days with the highest concentrations (comparing the top 5% of days with the lowest 50% of days). An SD increase in Cupressaceae concentrations was associated with a 1% decrease in ED visits. The association for Quercus species pollen was strongest for children aged 5 to 17 years. Effects of Ambrosia species pollen on asthma exacerbations were difficult to assess in this large-scale temporal analysis because of possible confounding by the steep increase in circulating rhinoviruses every September. Poaceae and Quercus species pollen contribute to asthma morbidity in Atlanta. Altered Quercus species and Poaceae pollen production caused by climate change could affect allergen-induced asthma morbidity in the southeastern United States. Copyright © 2012 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.