The internal structure of Diesel fuel injectors is known to have a significant impact on the nozzle flow and the resulting spray emerging from each hole. In this paper the three-dimensional transient flow structures inside a Diesel injector is studied under nominal (in-axis) and realistic (including off-axis lateral motion) operating conditions of the needle. Numerical simulations are performed in the commercial CFD code CONVERGE, using a two-phase flow representation based on a mixture model with Volume of Fluid (VOF) method. Moving boundaries are easily handled in the code, which uses a cut-cell Cartesian method for grid generation at run time. First, a grid sensitivity study has been performed and mesh requirements are discussed. Then the results of moving needle calculations are discussed. Realistic radial perturbations (wobbles) of the needle motion have been applied to analyze their impact on the nozzle flow characteristics. Needle radial motions are based on high-speed X-ray phase-contrast imaging collected at Argonne National Laboratory. Different types of wobbles are presented and the results are compared to the nominal in-axis motion behavior. Hole-to-hole differences are discussed and quantified. Complex flow structures are observed in the sac region of the nozzle and an explanation for the different flow structures emerging from each hole is provided. From this work it has been observed that in presence of needle wobble, at low and medium lifts hole-to-hole differences are observed. Also, some holes exhibits swirling flow which affects the near nozzle jet structure, the liquid mass distribution and the mass flow rate, resulting in potential spray modifications.