Large-eddy simulation (LES) has been performed for a single-cylinder, two-valve, four-stroke-cycle piston engine through 70 consecutive motored cycles. Initial comparisons of ensemble-averaged velocity fields have been made between LES and experiment, and proper orthogonal decomposition (POD) has been used to analyze the complex in-cylinder turbulent flows. Convergence of POD modes has been quantified, several POD variants have been explored, and sensitivity of results to analyzing different subsets of engine cycles has been studied. In general, it has been found that conclusions that were drawn earlier from POD analysis of a simplified non-compressing piston-cylinder assembly with a fixed valve carry over to the much more complex flow in this motored four-stroke-cycle engine. For the cases that have been examined, the first POD mode essentially corresponds to the ensemble-averaged mean velocity. The number of engine cycles required to extract converged POD modes increases with mode number, and varies with phase (piston position). There is little change in the lower-order phase-invariant POD modes when as few as 24 phases per cycle (30A degrees between samples) are used, and complex 3-D time-dependent in-cylinder velocity fields through full engine cycles can be reconstructed using a relatively small number of POD modes. Quantification of cycle-to-cycle variations and insight into in-cylinder flow dynamics can be extracted through analysis of phase-invariant POD modes and coefficients.