An experimental study is performed to investigate the effects of charge motion control on flow measurement inside an internal combustion (IC) engine assembly. Molecular Tagging Velocimetry (MTV) is used to obtain the multiple point measurement of the instantaneous velocity field. MTV is a molecular counterpart of PIV based techniques, and it eliminates the use of seed particles. A two-dimensional velocity field is obtained at various crank angle degrees (CADs) for tumble and swirl measurement planes inside an optical engine assembly [1500 and 2500 rpm engine speeds]. Effects of charge motion control are studied considering different cases of: (i) Charge motion control valve (CMCV) deactivated and (ii) CMCV activated. Both the measurement planes are used in each case to study the cycle-to-cycle variability inside an engine cylinder. Probability density functions (PDFs) of the normalized circulation (NC) are calculated from the instantaneous planar velocity to quantify the cycle-to-cycle variations of in-cylinder flows. Different geometries of CMCV produce different effects on the in-cylinder flow field. It is found that the CMCV used in this work has a profound effect on fuel-air mixing; however, its influence is not as significant during the late compression. Therefore, it can be assumed that CMCV has less contribution to enhance the flame speed during the combustion process.