Proper orthogonal decomposition (POD) is a coherent structure identification technique based on either measured or computed data sets. Recently, POD has been adopted for the analysis of the in-cylinder flows inside internal combustion engines. In this study, stereoscopic particle image velocimetry (Stereo-PIV) measurements were carried out at the central vertical tumble plane inside an engine cylinder to acquire the velocity vector fields for the in-cylinder flow under different experimental conditions. Afterwards, the POD analysis were performed firstly on synthetic velocity vector fields with known characteristics in order to extract some fundamental properties of the POD technique. These data were used to reveal how the physical properties of coherent structures were captured and distributed among the POD modes, in addition to illustrate the difference between subtracting and non-subtracting the ensemble average prior to conducting POD on datasets. Moreover, two case studies for the in-cylinder flow at different valve lifts and different pressure differences across the air intake valves were presented and discussed as the effect of both valve lifts and pressure difference have not been investigated before using phase-invariant POD analysis. The results demonstrated that for repeatable flow pattern, only the first mode was sufficient to reconstruct the physical properties of the flow. Furthermore, POD analysis confirmed the negligible effect of pressure difference and subsequently the effect of engine speed on flow structures. © 2018 by the authors.