Uncertainty and sensitivity analysis is an indispensable element of any substantial attempt in reactor simulation validation. A Coordinated Research Program (CRP) supervised by the International Atomic Energy Agency was started to investigate the various uncertainty quantification methodologies for High Temperature Gas-cooled Reactors. The first phase of the CRP is dedicated to the estimation of cell and lattice model uncertainties due to the neutron cross sections. Phase II is oriented towards the investigation of propagated uncertainties from the lattice to the coupled neutronics/thermal hydraulics core calculations. Best-estimate results for the prismatic single block (Ex. I-2a) and super cell models (Ex. I-2c) were obtained using the SCALE 6.2.0 two-dimensional lattice code NEWT. A reference spectrum was obtained with Serpent 2.1.27 for the single block, super cell and core models. The flux spectrum in the system of interest plays a primary role in the quantification of uncertainties caused by cross sections. In this work, the TRITON/NEWT-flux-weighted cross sections obtained for Ex. I-2a and various models of Ex.I-2c are utilized to perform a sensitivity analysis of the MHTGR-350 core power densities and eigenvalues. The core solutions are obtained with the Idaho National Laboratory (INL) coupled code PHISICS/RELAP5-3D. It is observed that axial shape of the core power density does not vary significantly with the various lattice cell libraries utilized. The use of cross section libraries originating from super cells induces changes of the core power density by 1–10% radially as compared to the Ex.I-2a cross sections. The magnitude of these variations increases as the moderator-to-fuel ratio increases in the super cell lattice models. A lattice flux spectrum resembling the core spectrum is hence necessary for correct predictions in nodal core calculations.