Engine running in has significant impact on tribological performance of the engine. This study investigated topographical changes of engine bores during running in experimentally and theoretically. Engine bores with various height distributions were generated by changing honing parameters. Engine running-in tests were conducted to observe changes of surface topography on engine bores. Surface height distributions were described by the Johnson translatory system. A running-in wear model was used to predict the progress of surface topography during engine running in. Comparisons between experimental and theoretical results show that the model used in this study can describe the topographical changes of running-in wear for surfaces with different height distributions.