This volume constitutes the refereed proceedings of the 13th International Workshop on Combinatorial Image Analysis, IWCIA 2009, held in Playa del Carmen, Mexico, in November 2009. The 32 revised full papers and one invited paper presented were carefully reviewed and selected from 70 initial submissions. The papers are organized in topical sections on digital geometry: curves, straightness, convexity, geometric transformations, metrics, distance transforms and skeletons, segmentation, thinning, skeletonization, image representation, processing, analysis, reconstruction and recognition, digital tomography, image models based on geometry, combinatorics, arithmetics, algebra, mathematical morphology, topology and grammars, as well as digital topology and its applications to image modeling and analysis.