We use a combined climate/chemistry model to assess the interannual variability of tropospheric ozone associated with the El Niño Southern Oscillation (ENSO). Simulations cover the years 1990 to 2001 with prescribed SSTs. El Niño and La Niña events are reproduced by the model. Previous studies have emphasized the impact of ENSO on tropospheric composition through changing emissions or convection. Here we show that there is a close relationship between ENSO and stratosphere-troposphere exchange (STE); different patterns of circulation and meteorology in El Niño and La Niña years result in significant differences in transport of ozone-rich air from the stratosphere to the troposphere. We calculate an anomalously large increase of STE following a typical El Niño year, most evident after the 1997–1998 El Niño event. La Niña events result in a decrease of STE. STE is one factor affecting tropospheric ozone; we find highest ozone after the 1997–1998 El Niño.