Abstract. This study uses the non-intrusive generalized polynomial chaos method to investigate the effects of uncertainties in the gas-surface interaction model on the hypersonic boundary layer flow over a flat plate. In particular, the polynomial chaos method is applied to assess uncertainties in the surface shear, normal stress, heat flux, flowfield temperature and density resulting from uncertain surface temperature and accommodation coefficient. The polynomial chaos approach allows us to estimate probability density functions from fewer flowfield samples than the traditional random Monte Carlo sampling. The flowfield solutions are computed by the DSMC code SMILE. The analysis shows that surface fluxes and flowfields in the hypersonic boundary layer are more sensitive to the accommodation coefficient than surface temperature uncertainty.