A combined numerical and experimental investigation is carried out to analyze the cycle-to-cycle variations (CCV) in an optically accessible spark-ignition engine with port fuel injection. A stable and an unstable operating condition is considered. Well-established turbulence, combustion, and ignition models are employed in the large-eddy simulations (LES). High-speed measurements of the velocity field via particle image velocimetry and flame imaging in the tumble plane are conducted in the experiments. A detailed comparison between LES and experiments is carried out, including the in-cylinder pressure, the flow fields, the spatial flame distribution, and the fields conditioned on fast and slow cycles. Good agreement is achieved for the variables considering all cycles; yet, some discrepancies are observed for the conditionally averaged quantities. A systematic quantitative correlation analysis between the selected influencing variables and the CCV is presented, in which the influencing variables are extracted from different length scales (r = 3 mm, 12 mm, and 43 mm) and the CCV are distinguished between the early flame kernel development and later flame propagation. Even though the most relevant influencing parameters are different for the two operating conditions, the location of the coherent vortex structure is found to be important for the CCV of both cases.