We present the results of airborne measurements of carbon monoxide (CO) and aerosol particle number concentration (CN) made during the Balanço Atmosférico Regional de Carbono na Amazônia (BARCA) program. The primary goal of BARCA is to address the question of basin-scale sources and sinks of CO<sub>2</sub> and other atmospheric carbon species, a central issue of the Large-scale Biosphere-Atmosphere (LBA) program. The experiment consisted of two aircraft campaigns during November–December 2008 (BARCA-A) and May 2009 (BARCA-B), which covered the altitude range from the surface up to about 4500 m, and spanned most of the Amazon Basin. <br><br> Based on meteorological analysis and measurements of the tracer, SF<sub>6</sub>, we found that airmasses over the Amazon Basin during the late dry season (BARCA-A, November 2008) originated predominantly from the Southern Hemisphere, while during the late wet season (BARCA-B, May 2009) low-level airmasses were dominated by northern-hemispheric inflow, and mid-tropospheric airmasses were of mixed origin. In BARCA-A we found strong influence of biomass burning emissions on the composition of the atmosphere over much of the Amazon Basin, with CO enhancements up to 300 ppb and CN concentrations approaching 10 000 cm<sup>−3</sup>; the highest values were in the southern part of the Basin at altitudes of 1–3 km. The ΔCN/ΔCO ratios were diagnostic for biomass burning emissions, and were lower in aged than in fresh smoke. Fresh emissions indicated CO/CO<sub>2</sub> and CN/CO emission ratios in good agreement with previous work, but our results also highlight the need to consider the residual smoldering combustion that takes place after the active flaming phase of deforestation fires. <br><br> During the late wet season, in contrast, there was little evidence for a significant presence of biomass smoke. Low CN concentrations (300–500 cm<sup>−3</sup>) prevailed basinwide, and CO mixing ratios were enhanced by only ~10 ppb above the mixing line between Northern and Southern Hemisphere air. There was no detectable trend in CO with distance from the coast, but there was a small enhancement of CO in the boundary layer suggesting diffuse biogenic sources from photochemical degradation of biogenic volatile organic compounds or direct biological emission. <br><br> Simulations of CO distributions during BARCA-A using a range of models yielded general agreement in spatial distribution and confirm the important contribution from biomass burning emissions, but the models evidence some systematic quantitative differences compared to observed CO concentrations. These mismatches appear to be related to problems with the accuracy of the global background fields, the role of vertical transport and biomass smoke injection height, the choice of model resolution, and reliability and temporal resolution of the emissions data base.