We have used the Whole Atmosphere Community Climate Model to produce a small (three‐member) ensemble of simulations of the period 1950–2003. Comparison of model results against available observations shows that for the most part, the model is able to reproduce well the observed trends in zonal mean temperature and ozone, both as regards their magnitude and their distribution in latitude and altitude. Calculated trends in water vapor, on the other hand, are not at all consistent with observations from either the HALOE satellite instrument or the Boulder, Colorado, hygrosonde data set. We show that such lack of agreement is actually to be expected because water vapor has various sources of low‐frequency variability (heating due to volcanic eruptions, the quasi‐biennial oscillation and El Niño–Southern Oscillation) that can confound the determination of secular trends. The simulations also reveal the presence of other interesting behavior, such as the lack of any significant temperature trend near the mesopause, a decrease in the stratospheric age of air, and the rare occurrence of an extremely disturbed Southern Hemisphere winter.