The thermospheric neutral density and ionospheric electron density day-to-day variations observed by the CHAMP satellite in 2006 are simulated by the NCAR-Thermosphere Ionosphere Mesosphere Electrodynamics General Circulation Model (TIMEGCM). It appears that these observed density daily variations are related to geomagnetic activity and solar EUV flux changes. The NCAR-TIMEGCM captures the observed thermospheric and ionospheric daily variability. These variations have periods of 5, 7, 9 and 11 and 13 days. Planetary waves from lower atmosphere by the TIMED/TIDI instruments are analyzed to study their contribution to the daily variations of the thermosphere and ionosphere. A diagnostic analysis of the outputs of TIMEGCM driven by ECWMF at its lower boundary is also carried out to investigate the mechanisms by which these different sources (geomagnetic activity, solar radiation changes and planetary waves) affect the upper atmosphere.