Recently Struchtrup (2013) proposed an extension to the original Maxwell boundary conditions for the Boltzmann equation which introduces velocity dependent accommodation coefficients. These boundary conditions are implemented into the direct simulation Monte Carlo (DSMC) method. The effect of the velocity dependent Maxwell (VDM) boundary conditions on thermal transpiration phenomena is studied for two-dimensional micro-cavities. Variation of the three microscopic parameters provided by the VDM boundary condition yields changes in slip velocity, temperature jump and the thermal transpiration effect. The results indicate that the strength of thermal transpiration can change and, depending on the values of the coefficients, the rarefied flow can be driven from warmer toward colder regions. (C) 2015 Elsevier Ltd. All rights reserved.