A direct simulation Monte Carlo technique is used to simulate the radiation heat transfer in a multiwafer low pressure chemical vapor deposition (LPCVD) reactor. The model accounts for the heat transfer between the stack of closely spaced Si wafers, the quartz reactor tube, the stainless steel ends of the reactor, and the surrounding furnace. Spectral and thermal variations in the materials properties are included directly in the model. In addition, conductive heat transfer through the quartz tube is computed using a finite difference approach. The cooled ends of the reactor result in a suppression of the temperature of several wafers at each end of the wafer stack. Simulations show that the extent of this cooling effect is influenced by direct radiative heat losses from the end wafers as well as dissipation of the furnace heat flux by conductive heat losses through the quartz tube. The calculated temperature profiles are then used as thermal boundary conditions in simulations of rarefied gas flows in the LPCVD reactor. The thermal variations along the quartz and wafer surfaces give rise to significant temperature and density variations in the gas flow. The simulation results show excellent agreement with experimental data.