A simulation of the middle atmosphere is presented using a General Circulation Model (GCM) forced with observed Sea Surface Temperature (SST) for the period 1950-2000. The GCM extends to the lower thermosphere and reproduces realistic dynamical and temperature distributions. The period contains several El Nino and La Nina 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 Nino events. These results are corroborated also by an annular mode analysis showing that the strongest coupling between stratosphere and troposphere is realized at the times of El Nino events when stratospheric sudden warmings are more frequent. In the Tropics, the effect of ENSO is to favor the injection of water vapor in stratosphere through the tropical tropopause during El Nino events.