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Cyclically loaded structural steel components are usually designed to endure macroscopic stress amplitudes close to the material’s endurance strength where microcracks initiate due to microstructural inhomogeneities and exhibit strong interactions with the various microstructural features in their neighborhood upon propagating. The current study presents a microstructural model with a capability to quantitatively describe the influence of microstructural features on the growth of cyclic cracks in the decisive, very early fatigue behavior stage. The FE model is based on the crystal plasticity theory and accounts for relative grain orientations. Both the extended finite element method (XFEM) and a coupled damage mechanics approach are used to describe crack opening behavior. The model is implemented to simulate real microcracking events produced in interrupted cyclic multiple-step tests under metallographic observation with temperature change measurements. Furthermore, the model is implemented on virtually created microstructures with altered grain sizes and orientations based on statistical EBSD analysis.