Cycle-to-cycle variability of intake-jet flow in an optical engine was measured using particle image velocimetry, revealing the possibility of two different flow patterns. A phase-dependent proper orthogonal decomposition analysis showed that one or the other flow pattern would appear in the average flow, sampled from test to test or sub-sampled within a single test; each data set contained individual cycles showing one flow pattern or the other. Three-dimensional velocity data from a large-eddy simulation of the engine showed that the particle image velocimetry plane cuts through a region of high shear between the intake jet and another large flow structure. Rotating the measurement plane 610°revealed one or the other flow structure observed in the particle image velocimetry measurements. Thus, it was hypothesized that cycle-to-cycle variations in the swirl ratio result in the two different flow patterns in the particle image velocimetry plane. Having an unambiguous metric to reveal large-scale flow cycle-to-cycle variability, causes for this variability were examined within the possible sources present in the available testing. In particular, variations in intake-port and cylinder pressure, lateral valve oscillations, and engine RPM were examined as potential causes for the cycle-to-cycle flow variations using the phase-dependent proper orthogonal decomposition coefficients. No direct correlation was seen between the intake-port pressure, or the pressure drop across the intake valve, and the in-cylinder flow pattern. A correlation was observed between dominant flow pattern and cycle-to-cycle variations in intake-valve horizontal position. RPM values and in-cylinder flow patterns did not correlate directly. However, a shift in flow pattern was observed between early and late cycles in a 2900-cycle test after an approximately 5 r/min engine speed perturbation.