A novel scheme is presented for incorporating finite thickness cohesive interfaces in virtual grain structures for crystal plasticity finite element (CPFE) analyses of intergranular crack initiation and propagation. A Voronoi tessellation model is used to define the virtual grain structure, with automatically generated nonzero thickness cohesive zones (CZs) representing the grain boundaries and multiple junctions. An efficient grain boundary offsetting algorithm is presented, and issues related to automatically partitioning multiple junctions are discussed. Two feasible junction partitioning schemes are presented, the second of which has the advantage of partitioning junctions using uniform quadrilateral elements and naturally defining their normal and tangential directions. For the second scheme, a rule-based method is presented that carries out the preliminary meshing of CZ junctions, including data representation, edge event processing, and cut and trim operations. A virtual grain structure modelling system, VGRAIN, is introduced to implement the proposed CZ junction partitioning method and directly generate meshed virtual grain structures with CZ grain boundaries for CPFE studies. To demonstrate the proposed junction partitioning and CZ representation schemes, two finite strain CPFE simulations are presented for plane strain uniaxial tension and three-point bending, demonstrating large-scale crack initiation and propagation under shear and opening modes. Copyright © 2012 John Wiley & Sons, Ltd.