The transport properties of nano-porous materials determine their applicability, e.g. as separators or catalysts (J. Ka¨rger, D. Ruthven. Diffusion in zeolites, Wiley, New York (1991); L.V.C. Rees, D. Shen. Adsorption of gases in zeolite molecular sieves. In Introduction to Zeolite Science and Practice, Studies in surface science and catalysis, H.V.C. van Bekkum, E.M. Flanigen, P.A. Jacobs, J.C. Jansen (Eds.), vol. 137, pp. 579–631, Elsevier, Amsterdam (2001)). Adsorption in zeolites is explained as a two-step process; adsorption to the external crystal surface and subsequent intra-crystalline diffusion (R. M. Barrer. Porous crystal membranes. J. Chem. Soc. Faraday Trans., 86, 1123 (1990)). Both steps have been considered to be isothermal (P. Kortunov, S. Vasenkov, C. Chmelik, J. Ka¨rger, D. Ruthven, J. Wloch. Influence of defects on the external crystal surface on molecular uptake into MFI-type zeolites. Chem. Mater., 16, 3552 (2004); J. Ka¨rger. Measurements of diffusion in zeolites—a never ending challenge? Adsorption, 9, 29 (2003)). Here we show, using non-equilibrium molecular dynamics simulations of n-butane in silicalite (J.M. Simon, A. Decrette, J.P. Bellat, J.M. Salazar. Kinetics of adsorption of n-butane on an aggregate of silicalite by transient non-equilibrium molecular dynamics. Mol. Simul., 30, 621 (2004)) that a significant temperature change accompanies adsorption and intra-crystalline transport, and leads to a significant varying thermal driving force across the crystal surface, in agreement with the proposition of Ruthven et al. (D.M. Ruthven, L.K. Lee. Kinetics of nonisothermal sorption: systems with bed diffusion control. AICHE J., 27, 654 (1981)). The butane flux into the crystal is caused in the first stage by a chemical potential difference. In the second stage the temperature of the zeolite decreases due to a thermal force across the surface. This slow reduction in the zeolite temperature induces a small butane uptake, that may help explain why equilibrium techniques give larger diffusion coefficients than non-equilibrium techniques (J. Ka¨rger. Measurements of diffusion in zeolites—a never ending challenge? Adsorption, 9, 29 (2003)). Descriptions of transport in nano-porous materials (J. Ka¨rger, D. Ruthven. Diffusion in zeolites, Wiley, New York (1991); R. Krishna, J. A. Wesselingh. The Maxwell–Stefan approach to mass transfer. Chem. Eng. Sci., 52, 861 (1997)) need to include a thermal driving force.