Large-eddy Simulations (LES) have been carried out to investigate spray variability and its effect on cycle-to-cycle flow variability in a direct-injection spark-ignition (DISI) engine under non-reacting conditions. Initial simulations were performed of an injector in a constant volume spray chamber. Detailed measurements of the spray including quantitative mixing data are used to validate a simulation spray set-up for the stepped-bore multi-hole gasoline direct injection (GDI) injector. A random seed perturbation methodology was used to generate shot-to-shot spray variability in the LES, and comparisons of both mean and standard deviations were made for quantities with sufficient experimental data. After validation, the same spray set-up was used to simulate the same injector in an optically accessible DISI engine. Particle Image Velocimetry (PIV) measurements were used to quantify the flow, including during the fuel injection period, which occurred during intake for the investigated operating condition. The engine was operated in a skip-fired operating mode and comparisons focused on cycles that included fuel injection, but no spark event and therefore no combustion. Multi-cycle LES is compared against the experimental results, focusing on the effects of spray variability and interaction effects with cyclic flow variability. Flow field comparisons are also made against previously published results of pure motored flow, i.e. without fuel injection.