Material microstructure plays a key role in crack initiation under rolling contact fatigue. When studying microstructure with crystal plasticity finite element method (CPFE), mesh sensitivity study is of great importance, as the surface-near region is under high uniaxial stresses. In this paper, a new structured mesh strategy is purposed and compared with the classical unstructured mesh strategy. Modelling tests on a bi-grain and a polycrystal model show the calculation of geometrically necessary dislocation (GND) density, recently proposed as a suitable fatigue damage indicator, is highly dependent on mesh morphology, when GND hotspots tend to appear near distorted elements even in homogeneous materials. With uniform mesh size and shape, structured mesh elements can provide physically more acceptable GND calculations, which is particularly important in loading scenarios with complex stresses, such as rolling contact fatigue. Computational efficiency is also improved compared to unstructured models because a smaller number of elements are required in a structured mesh model and pre-processing of the mesh is not required.