We have studied the effects of the 2006 El Niño on tropospheric O3 and CO at tropical and sub-tropical latitudes measured from the OMI and MLS instruments on the Aura satellite. The 2006 El Niño-induced drought caused forest fires (largely set to clear land) to burn out of control during October and November in the Indonesian region. The effects of these fires are clearly seen in the enhancement of CO concentration measured from the MLS instrument. We have used a global model of atmospheric chemistry and transport (GMI CTM) to quantify the relative importance of biomass burning and large scale transport in producing observed changes in tropospheric O3 and CO. The model results show that during October and November biomass burning and meteorological changes contributed almost equally to the observed increase in tropospheric O3 in the Indonesian region. The biomass component was 4–6 DU but it was limited to the Indonesian region where the fires were most intense. The dynamical component was 4–8 DU but it covered a much larger area in the Indian Ocean extending from South East Asia in the north to western Australia in the south. By December 2006, the effect of biomass burning was reduced to zero and the observed changes in tropospheric O3 were mostly due to dynamical effects. The model results show an increase of 2–3% in the global burden of tropospheric ozone. In comparison, the global burden of CO increased by 8–12%.