Haemodynamics, and in particular wall shear stress, is thought to play a critical role in the progression and rupture of intracranial aneurysms. A novel method is presented that combines image-based wall motion estimation obtained through non-rigid registration with computational fluid dynamics (CFD) simulations in order to provide realistic intra-aneurysmal flow patterns and understand the effects of deforming walls on the haemodynamic patterns. In contrast to previous approaches, which assume rigid walls or ad hoc elastic parameters to perform the CFD simulations, wall compliance has been included in this study through the imposition of measured wall motions. This circumvents the difficulties in estimating personalized elasticity properties. Although variations in the aneurysmal haemodynamics were observed when incorporating the wall motion, the overall characteristics of the wall shear stress distribution do not seem to change considerably. Further experiments with more cases will be required to establish the clinical significance of the observed variations.