Vertical profiles of isoprene, methanol, and ozone (O3) concentrations were measured between the middle and upper atmospheric boundary layer (ABL) from a research aircraft and were numerically simulated for the ABL and a deciduous forest canopy with a one-dimensional model coupling turbulence diffusion and atmospheric chemistry. Isoprene emissions from the deciduous forest canopy were estimated by coupling an existing biogenic emission algorithm with estimates of canopy leaf density inferred from satellite remote sensing observations. Numerical simulations predicted low isoprene concentrations in the middle and upper ABL; however, the agreement between the simulations and the measured values was poor for two of the three profiles, indicating that a three-dimensional transport model might be necessary in future simulations. Chemical oxidation of isoprene by O3 and hydroxyl radical (OH), particularly in the middle and upper ABL, tends to reduce the isoprene concentrations and influences the vertical fluxes in that layer; however, chemical reactions have little effect on fluxes of isoprene near the emission source, where turbulent mixing is much faster than chemical reactions and where the emission process controls the vertical flux. The isoprene flux decreases rapidly with increasing height, with little isoprene escaping from the ABL. Vertical profiles of methanol concentrations were simulated with the biogenic emission algorithm used for isoprene; these vertical profiles were similar to the measured values for the well-mixed ABL but were much lower than the measured concentrations in the lower layers of the growing ABL because of weaker calculated mixing in the upper ABL during the morning. The results of this investigation indicate that chemical oxidation of isoprene is rapid enough to allow O3 and other oxidants to accumulate in the ABL on a regional scale if sufficient levels of nitrogen oxides are present; however, methanol is much more stable, and biogenic emissions of this compound have the potential to form O3 and other oxidants in areas distant from the emission source. ¿ 1999 American Geophysical Union