Ever decreasing permitted emission levels and the necessity of more efficient engines demand a better understanding of in-cylinder phenomena. In swirl-supported compression ignition (CI) engines, mean in-cylinder flow structures formed during the intake stroke deeply influence mixture preparation prior to combustion, heat transfer and pollutant oxidation all of which could potentially improve engine performance. Therefore, the ability to characterize these mean flow structures is relevant for achieving performance improvements. CI mean flow structure is mainly described by a precessing vortex. The location of the vortex center is key for the characterization of the flow structure. Consequently, this work aims at evaluating algorithms that allow for the location of the vortex center both, in ensemble-averaged velocity fields and in instantaneous velocity fields. The study is carried out on velocity fields measured using Particle Image Velocimetry (PIV) in an optical light-duty CI engine operated under motored conditions. The algorithms are applied to both ensemble-averaged and instantaneous velocity fields, to evaluate the robustness of the different approaches. When used for instantaneous velocity fields, algorithms based on velocity field’s magnitudes are less robust and might fail to locate the vortex center. On the contrary, an algorithm based on the velocity field topology successfully locate the vortex center location.