In situ aircraft measurements of trace gases and aerosols were made in the boundary layer (BL) and free troposphere (FT) over Indonesia and Australia during the Biomass Burning and Lightning Experiment (BIBLE)-A and B conducted in August-October 1998 and 1999. Concentrations of ozone (O3) and its precursors [CO, reactive nitrogen (NOx), non-methane hydrocarbons (NMHCs)] were measured in these campaigns to identify the sources of NOx and to estimate the effects of biomass burning and lightning on photochemical production of O3. Over Indonesia, in-situ production of NOx by lightning was found to be a major source of reactive nitrogen in the upper troposphere during BIBLE-A. In some circumstances, increases in reactive nitrogen were often associated with enhancements in CO and NMHCs, suggesting that the sources were biomass burning and fossil fuel combustion, followed by upward transport by cumulus convection. Over Australia the levels of O3, CO, reactive nitrogen, and NMHCs were elevated throughout the troposphere compared to those observed in the tropical Pacific. However, the mechanisms responsible for the enhanced concentrations in the BL and FT are distinctly different. The emissions from biomass burning that occurred in northern Australia were restricted to the BL because of strong subsidence in the period. In the FT over Australia, elevated concentrations of O3 and its precursors result from injections of emissions as the air masses travel over Africa, South America, the Indian Ocean, and Indonesia en route to Australia. In all cases, O3 levels in the biomass burning plumes were enhanced due to photochemical production.