Selected gas pulse tests on initially saturated claystone samples under isotropic confinement pressure are simulated using a 3D thermo-hydro-mechanical code. The constitutive model considers the hydro-mechanical anisotropy of argillaceous rocks. A cross-anisotropic linear elastic law is adopted for the mechanical behaviour. Elements for a proper modelling of gas flow along preferential paths include an embedded fracture permeability model. Rock permeability and its retention curve depend on strains through a fracture aperture. The hydraulic and mechanical behaviours have a common anisotropic structure. Small-scale heterogeneity is considered to enhance the initiation of flow through preferential paths, following the direction of the bedding planes. The numerical simulations were performed considering two different bedding orientations, parallel and normal to the imposed flow in the test. Simulations are in agreement with recorded upstream and downstream pressures in the tests. The evolution of fluid pressures, degree of saturation, element permeability and stress paths are presented for each case analysed. This information provides a good insight into the mechanisms of gas transport. Different flow patterns are obtained depending on bedding orientation, and the results provide an explanation for the results obtained in the tests. Copyright © 2012 John Wiley & Sons, Ltd.