Nearly two years of tropospheric O3 and H2O data from the Aura Ozone Monitoring Instrument (OMI) and Microwave Limb Sounder (MLS) instruments are analyzed to study the characteristics of intra-seasonal oscillation (ISO) of 20–100 day periods. The analysis shows the presence of ISO signals in O3 and H2O throughout much of the tropics including the north Atlantic not shown in previous studies. ISO variability west of the dateline appears as a manifestation of eastward propagation of the Madden-Julian Oscillation (MJO). Time series of tropospheric O3 and H2O are negatively correlated throughout much of the tropics, and mostly over ocean. This suggests lofting of air from convection as a basic driving mechanism, with convection transporting low amounts of O3 and high amounts of H2O upwards from the boundary layer. ISO/MJO related changes in O3 and H2O are a major source of variability and often exceed 25% of background concentrations.