These proceedings contain the papers selected for presentation at the third edition of the International Workshop on Conceptual Modeling in GIS, CoMoGIS 2006, held in November 2006, in Tucson, Arizona, USA, in conjunction with the annual International Conference on Conceptual Modeling (ER 2006). Following the success of CoMoGIS 2005 (held in Klagenfurt, Austria) and CoMoGIS 2004 (held in Shanghai, China), its aim was to bring together researchers investigating issues related to conceptual modeling for geographic and spatial information handling systems, and to encourage interdisciplinary discussions including the identification of emerging and future issues. The call for papers attracted 19 papers, many of them of excellent quality and most of them very related to the topics of the workshop. Each paper received three reviews. Based on these reviews, eight papers were selected for presentation and inclusion in the proceedings. The accepted papers cover a wide range of topics from spatial and spatio-temporal data representation, to indexing methods for moving objects, to optimization of spatial queries and to spatio-temporal data on the Web. Our keynote presentation, given by Peter Baumann, discussed large-scale raster services.