The effects of uncertainties in the gas-surface and intermolecular interaction models on a hypersonic boundarylayer development are investigated by propagating these uncertainties through direct simulation Monte Carlo calculations of Mach 10 and 20 flows. The model input uncertainties considered are the momentum accommodation coefficient in the Maxwellian gas-surface interaction model, surface temperature and the viscosity exponent in the variable hard sphere molecular model. The effects of the input uncertainties are quantified by computing produced uncertainties in the flowfield temperature, flowfield density, surface shear, pressure, and heat flux. A nonintrusive generalized polynomial chaos expansion is used to propagate the uncertainties; reconstruct the probability density functions; and calculate the mean, standard deviation, and skewness of the output variables. It is shown that the polynomial chaos expansion with just three flowfield samples can propagate uncertainties with an accuracy equivalent to Monte Carlo methods with 10 million samples. The uncertainty analysis shows that the surface fluxes and the flowfields in the hypersonic boundary layer are more sensitive to the accommodation coefficient uncertainty than surface temperature or viscosity exponent uncertainty. An input uncertainty of 19% in the accommodation coefficient results in a 20% uncertainty in the flowfield temperature at Mach 10 and a 31% uncertainty at Mach 20. This input uncertainty results in 22 and 28% uncertainties in the surface fluxes at the two Mach numbers. The produced uncertainties generally increase with Mach number, and the effect of introduced uncertainty diminishes away from the leading edge. Nomenclature a n = generalized polynomial chaos expansion coefficient C = Chapman-Rubesin constant w T 1 = 1 T w f y = probability distribution function of a dependent variable f z = probability distribution function of an independent variable I = order of Gaussian expansion M = Mach number N = order of the generalized polynomial chaos expansion N s = number of samples Re x = Reynolds number based on distance from leading edge T r = rotational temperature T t = translational temperature T w = wall temperature T 1 = freestream temperature V = rarefaction parameter M C=Re x p w i = Gaussian weight x = spatial coordinate Y = direct simulation Monte Carlo output y = independent variable y = mean of an independent variable Z = independent random variable with an arbitrary interval z = independent random variable scaled to 1; 1 interval = momentum accommodation coefficient = skewness of a dependent variable = mean free path w = coefficient of viscosity at wall temperature 1 = coefficient of viscosity at freestream temperature = density = standard deviation of a dependent variable n = orthogonal polynomial of order n ! = viscosity exponent in variable hard sphere model