Dislocation configurational energy and stored energy densities are determined in discrete dislocation and crystal plasticity modelling respectively and assessed with respect to experiments on single crystal nickel fatigue crack nucleation. Direct comparisons between the three techniques are provided for two crystal orientation fatigue tests. These provide confirmation that both quantities correctly identify the sites of fatigue crack nucleation and that stored energy density is a reasonable approximation to the more rigorous dislocation configurational energy. GND density is shown to be important in locating crack nucleation sites because of its role in the local configurational energy density. •Integrated experimental and computational study of fatigue crack nucleation in two nickel single crystals using discrete dislocation plasticity and crystal plasticity.•Successful identification of the crack nucleation sites in both single crystals using the configurational energy density from discrete dislocation plasticity and the stored energy density from crystal plasticity.•GND density plays a significant role in the identification of crack nucleation sites at the micron length scale.•Microstructural quantities such as lattice rotation, principle stress, effective strain and SSD density cannot in their own right predict the crack initiation sites.