A tethered balloon-sampling platform was used to study biogenic volatile organic compounds (BVOCs) in the atmospheric boundary layer in three distinct moist tropical forest ecoregions, as well as an extensive pasture area, in Amazonia. Approximately 2440 soundings, including as many as four VOC samples collected simultaneously at various altitudes, were made at each site. Concentrations in the mixed layer increased during morning hours and were relatively constant midday through afternoon. Since most important meteorological and chemical parameters were very similar among the sites during the measurement periods, a BVOC canopy emission model was used with a model of the chemistry of the boundary layer to reproduce the atmospheric concentrations observed. The simulations indicated significantly different midday landscape isoprene and α-pinene emission rates for the three forest ecoregions (2200, 5300, 9800 μg m-2h-1 isoprene and 90, 120, and 180 μg m-2 h-1 x-pinene for the three moist forest ecoregions studied, respectively). The differences in emissions among the ecoregions may be attributed to the species composition, which were markedly different and in which the percentage of isoprene and terpene emitting species also differed significantly. © 2004 Blackwell Publishing Ltd.