The early stages of the formation of dislocation microstructures in low strain fatigue are analysed,using three-dimensional discrete dislocation dynamics modelling (DDD). A detailed analysis of the simulated microstructures provide a detailed scheme for the persistent slip band formation, emphasizing the crucial role of cross-slip for both the initial strain spreading inside of the grain and for the subsequent strain localization in the form of slip bands. A new ad-hoc post-treatment tool evaluates the surface roughness as the cycles proceed. Slip markings and their evolutions are analysed, in relation to the dislocation microstructure. This dislocation-based study emphasizes the separate contribution of plastic slip in damage nucleation. A simple ID dislocation based model for work-hardening in crystal plasticity is proposed. In this model, the forest dislocations are responsible for friction stress (isotropic work-hardening), while dislocation pile-ups and dislocation trapped in Persistent Slip Bands (PSB) produce the back stress (kinematic work-hardening). The model is consistent with the stress-strain curves obtained in DDD. It is also consistent with the stress-strain curves experimentally obtained for larger imposed strain amplitudes.