A simulation of the middle atmosphere is presented using a general circulation model (GCM) forced with observed sea surface temperature for the period 1950–2000. The GCM extends to the lower thermosphere and reproduces realistic dynamical and temperature distributions. The period contains several El Niño and La Niña events, which are identified using the NINO3 index. Composite anomalies of relevant meteorological fields are obtained by stratifying the northern winter season according to the NINO3 index. These anomalies have the structure of vertically propagating planetary waves extending from the troposphere to the mesosphere. Circulation anomalies in the middle atmosphere are accompanied by large temperature anomalies that are of opposite sign in the stratosphere and mesosphere, the former being warmer and the latter colder during El Niño events. Near the summer mesopause, changes in momentum deposition by parameterized gravity waves results in warming during El Niño. Detailed statistical analysis is used to determine the significance of these anomalies. A chemical/transport simulation is carried out using output from the GCM. It shows that when the lower stratosphere is colder (as during La Niña events), some ozone depletion takes place. Conversely, when the lower stratosphere is warmer and more disturbed, as is the case during El Niño events, heterogeneous chemical processes are inhibited.