A comparative study of the limit of predictability in the stratosphere and troposphere in a coupled general circulation model is carried out using the National Center for Environmental Prediction (NCEP) Climate Forecast System Interactive Ensemble (CFSIE). In “identical twin experiments”, we compare the forecast errors of zonal wind and potential temperature in the troposphere and stratosphere for various wave groups. The results show smaller intrinsic error growth in the lower stratosphere compared with troposphere. The limit of predictability of sudden stratospheric warming events, measured by the errors in the divergence of the Eliassen‐Palm flux, is dominated by the amplification of small errors in the individual fields due to differences between the phase of the waves.