The numerical method based on event-driven molecular dynamics (EDMD) algorithm was developed for investigation of free-molecular and transitional gas flows in regions with arbitrary boundaries. Method was applied to two classical problems of rarefied gas dynamics: (1) transitional gas flow through plane channel of finite length between two reservoirs with small pressure difference, (2) supersonic flow past cylinder. These very different problems were chosen in order to study efficiency and applicability limits of the EDMD method for rarefied gas dynamics. The importance of the EDMD approach for rarefied gas dynamics is that EDMD is fully deterministic meshless implementation of chosen collision model without stochastic collision pair selection (unlike direct simulation Monte-Carlo method) or simplification of the collision integral (unlike model equations methods). So it gives additional information for the analysis of mechanical model itself with no regard to the features of the algorithm and can be used for verification of other numerical methods.