The atmospheric circulation acts as a bridge between large-scale sources of climate variability, and climate variability on regional scales. Here a statistical method is applied to monthly mean Southern Hemisphere 500hPa geopotential height to separate the interannual variability of the seasonal mean into intraseasonal and slowly varying (time scales of a season or longer) components. Intraseasonal and slow modes of variability are estimated from realisations of models from the Coupled Model Intercomparison Project Phase 3 (CMIP3) twentieth century coupled climate simulation (20c3m) and are evaluated against those estimated from reanalysis data. The intraseasonal modes of variability are generally well reproduced across all CMIP3 20c3m models for both Southern Hemisphere summer and winter. The slow modes are in general less well reproduced than the intraseasonal modes, and there are larger differences between realisations than for the intraseasonal modes. New diagnostics are proposed to evaluate model variability. It is found that differences between realisations from each model are generally less than inter-model differences. Differences between model-mean diagnostics are found. The results obtained are applicable to assessing the reliability of changes in atmospheric circulation variability in CMIP3 models and for their suitability for further studies of regional climate variability.