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The impact of biomass burning aerosol (BBA) on the regional climate in South America is assessed using 30-year simulations with a global atmosphere-only configuration of the Met Office Unified Model. We compare two simulations of high and low emissions of biomass burning aerosol based on realistic interannual variability. The aerosol scheme in the model has hygroscopic growth and optical properties for BBA informed by recent observations, including those from the recent South American Biomass Burning Analysis (SAMBBA) intensive aircraft observations made during September 2012. We find that the difference in the September (peak biomass emissions month) BBA optical depth between a simulation with high emissions and a simulation with low emissions corresponds well to the difference in the BBA emissions between the two simulations, with a 71.6% reduction from high to low emissions for both the BBA emissions and the BB AOD in the region with maximum emissions (defined by a box of extent 5-25 degrees S, 40-70 degrees W, used for calculating mean values given below). The cloud cover at all altitudes in the region of greatest BBA difference is reduced as a result of the semi-direct effect, by heating of the atmosphere by the BBA and changes in the atmospheric stability and surface fluxes. Within the BBA layer the cloud is reduced by burnoff, while the higher cloud changes appear to be responding to stability changes. The boundary layer is reduced in height and stabilized by increased BBA, resulting in reduced deep convection and reduced cloud cover at heights of 914 km, above the layer of BBA. Despite the decrease in cloud fraction, September downwelling clear-sky and all-sky shortwave radiation at the surface is reduced for higher emissions by 13.77 +/- 0.39 W m(-2) (clear-sky) and 7.37 +/- 2.29 W m(-2) (all-sky), whilst the upwelling shortwave radiation at the top of atmosphere is increased in clear sky by 3.32 +/- 0.09 W m(-2), but decreased by -1.36 +/- 1.67 W m(-2) when cloud changes are included. Shortwave heating rates increase in the aerosol layer by 18% in the high emissions case. The mean surface temperature is reduced by 0.14 +/- 0.24 degrees C and mean precipitation is reduced by 14.5% in the peak biomass region due to both changes in cloud cover and cloud microphysical properties. If the increase in BBA occurs in a particularly dry year, the resulting reduction in precipitation may exacerbate the drought. The position of the South Atlantic high pressure is slightly altered by the presence of increased BBA, and the strength of the southward low-level jet to the east of the Andes is increased. There is some evidence that some impacts of increased BBA persist through the transition into the monsoon, particularly in precipitation, but the differences are only statistically significant in some small regions in November. This study therefore provides an insight into how variability in deforestation, realized through variability in biomass burning emissions, may contribute to the South American climate, and consequently on the possible impacts of future changes in BBA emissions.