Molecular dynamics techniques have been used to simulate the diffusion of n-heptane, 2-methyl-hexane, 2,3-dimethylpentane, 1-propyl-2-methyl-cyclopropane, and 1-isopropyl-2methyl-cyclopropane in two unidimensional medium pore zeolites, ZSM-48 and Theta-1. In this way the isomerisation reactions n-heptane --> 2-methyl-hexane --> 2,3-dimethyl-pentane were studied, also including the cyclopropane reaction intermediates. The self-diffusivity of these sorbates and its variation with the channel size of the zeolite is studied. The diffusion in the slightly larger channels of ZSM-48 is faster than that found in Theta-1, and an effect of product shape selectivity, especially in Theta-1, is observed in the reaction going from the monomethyl to the dimethyl isomer. An excess of the monobranched/dibranched ratio is then expected in Theta-1 with respect to ZSM-48. The role of the external versus internal surface in the reaction products has been investigated by carrying out catalytic isomerisation of n-hexadecane in Theta-1 by depleting the external surface of acid sites. The results show that terminal monobranched alkanes can be formed inside the pores, and that dibranched alkanes are mainly formed at the external surface by isomerisation of the monobranched products.