Transport theory (Sn) calculations of the Ultra High Temperature Reactor Experiment (UHTREX) are compared with results obtained in clean cold critical experiments. These experiments are characterized by a high (43% of all neutrons produced) fast neutron leakage from the core, a hardened thermal neutron spectrum (a reactivity effect of −9.5% compared to a Maxwellian spectrum at the same temperature) and two spatial self-shielding effects. The smaller of the self-shielding effects, −2% in reactivity, occurs in the coated fuel particles contained in the fuel elements. A larger spatial self-shielding effect, −3.6% in reactivity, results from the heterogeneous arrangement of fuel elements and core moderator. The radial fuel channel design and radially graduated fuel loading complicate the calculation of the fuel element self-shielding because the entire core cannot be represented by one simple unit cell. However, conventional cell homogenization techniques are adequate when applied to subregions of the core. In spite of the geometrical complexities, the calculated multiplication factors and fission distributions agree well with experiment.