Abstract Background Characterizing multipollutant health effects is challenging. We use classification and regression trees to identify multipollutant joint effects associated with pediatric asthma exacerbations and compare these results with those from a multipollutant regression model with continuous joint effects. Methods We investigate the joint effects of ozone, NO 2 and PM 2.5 on emergency department visits for pediatric asthma in Atlanta (1999–2009), Dallas (2006–2009) and St. Louis (2001–2007). Daily concentrations of each pollutant were categorized into four levels, resulting in 64 different combinations or “Day-Types” that can occur. Days when all pollutants were in the lowest level were withheld as the reference group. Separate regression trees were grown for each city, with partitioning based on Day-Type in a model with control for confounding. Day-Types that appeared together in the same terminal node in all three trees were considered to be mixtures of potential interest and were included as indicator variables in a three-city Poisson generalized linear model with confounding control and rate ratios calculated relative to the reference group. For comparison, we estimated analogous joint effects from a multipollutant Poisson model that included terms for each pollutant, with concentrations modeled continuously. Results and discussion No single mixture emerged as the most harmful. Instead, the rate ratios for the mixtures suggest that all three pollutants drive the health association, and that the rate plateaus in the mixtures with the highest concentrations. In contrast, the results from the comparison model are dominated by an association with ozone and suggest that the rate increases with concentration. Conclusion The use of classification and regression trees to identify joint effects may lead to different conclusions than multipollutant models with continuous joint effects and may serve as a complementary approach for understanding health effects of multipollutant mixtures.