Total electron content (TEC) measurements from ground stations to Global Positioning System (GPS) satellites provide a rich source of information about the Earth's ionosphere. These data comprise a significant part of the typical data set used by various data ingestion and assimilation models of the ionosphere. For example, the Utah State University (USU) Global Assimilation of Ionospheric Measurements (GAIM) data assimilation model uses slant TEC, along with various other types of data, to obtain a global reconstruction of the ionosphere. There are presently two different USU GAIM models: the Gauss‐Markov Kalman Filter (GAIM‐GM), which is operational at the NASA Community Coordinated Modeling Center and the Air Force Weather Agency; and the Full‐Physics Kalman Filter (GAIM‐FP), which is presently run for scientific studies. TEC is the integrated electron density along the path from the ground to the GPS satellites, which orbit at approximately 20,200 km. The GAIM‐FP modeled space ranges up to 30,000 km in altitude, so the entire TEC raypath is contained within the model space. Many ionosphere models do not model this entire region. For example, the GAIM‐GM extends up to an altitude of 1400 km. It is necessary to account for the portion of TEC that is not modeled by some means. There are basically two simple techniques that are in common use: (1) correct the measured TEC by using a model of the upper ionosphere and plasmasphere to subtract their contributions, or (2) ignore the effect and assign the full measured TEC to the ionosphere within the assimilation model space. We present the effect of assimilating TEC measurements into the GAIM‐GM using both the techniques mentioned above. It is found that derived quantities such as N m F 2 are significantly degraded by ignoring the upper ionospheric contribution to TEC. This degradation is seen at all local times. The effect is most pronounced at night, when the F region densities are small and the upper ionospheric contribution to TEC is relatively large.