Hierarchical modeling is becoming increasingly popular in epidemiology, particularly in air pollution studies. When potential confounding exists, a multilevel model yields better power to assess the independent effects of each predictor by gathering evidence across many sub-studies. If the predictors are measured with unknown error, bias can be expected in the individual substudies, and in the combined estimates of the second-stage model. We consider two alternative methods for estimating the independent effects of two predictors in a hierarchical model. We show both analytically and via simulation that one of these gives essentially unbiased estimates even in the presence of measurement error, at the price of a moderate reduction in power. The second avoids the potential for upward bias, at the price of a smaller reduction in power. Since measurement error is endemic in epidemiology, these approaches hold considerable potential. We illustrate the two methods by applying them to two air pollution studies. In the first, we re-analyze published data to show that the estimated effect of fine particles on daily deaths, independent of coarse particles, was downwardly biased by measurement error in the original analysis. The estimated effect of coarse particles becomes more protective using the new estimates. In the second example, we use published data on the association between airborne particles and daily deaths in 10 US cities to estimate the effect of gaseous air pollutants on daily deaths. The resulting effect size estimates were very small and the confidence intervals included zero.