The global numerical upper atmosphere model (UAM) has been used to investigate the effects of the April 2002 magnetic storms on the Earth’s ionosphere and thermosphere. Results of UAM simulations have been compared with experimental plasma density and temperatures obtained by seven incoherent scatter radars and with neutral composition and temperature data provided by the NRLMSISE-00 model. The UAM calculations of plasma density and temperatures were performed using three versions of neutral constituents: (1) the NRLMSISE-00 neutral composition and temperature; (2) fully self-consistently determined theoretical neutral composition and temperature obtained using NRLMSISE-00 as an initial condition; (3) the same as in (2) but with simulations starting from the steady state theoretical thermosphere solution as an initial condition on April 15, 2002. The model calculations with the “theoretical thermosphere” give a larger thermospheric response to the magnetic storm (neutral temperature increase and O/N2 ratio decrease) and a more distinct negative ionospheric storm effect than the calculations with the NRLMSISE, resulting in N e, T i and T e calculations closer to the radar observations. In most cases, when the model used the MSIS-specified neutral atmosphere, it performed the worst, indicating that an interactive thermosphere is needed to model the ionosphere accurately.