An analysis is presented of vertical profiles of isoprene concentration and meteorological parameters measured in the boundary layer (BL) during the daylight hours at a rural site in Alabama and an urban site in Atlanta, Georgia, during the summer of 1990, as part of the Southern Oxidants Study. Of the 37 isoprene profiles recorded at the sites, 16 exhibited complex vertical structure with local maxima within the BL. This complex vertical structure appears to arise from a variety of turbulent processes fostered by horizontal inhomogeneities in the surface emissions of isoprene and by the transient appearance of layers of strong wind shear and/or vertical stability within the BL. A statistical analysis of the data suggests that the complex features observed in the individual profiles are stochastic in nature and tend to cancel out upon averaging over all profiles. Nevertheless, these complex structures can confound attempts to infer the BL abundance of a short-lived hydrocarbon like isoprene from a set of measurements at a single height. Our calculations suggest that measurements made at a height of 40–100 m above the surface will yield the most reliable measure of average BL concentrations of reactive hydrocarbons.