Urban meteorological modeling has become more realistic within the last decade with the availability of increased computer power. Accurate modeling of the urban zone is critical, as increasing fractions of the global population concentrate in cities. Accurate modeling can thus reduce adverse impacts on populations resulting from a variety of urban weather and air quality impacts, ranging from flooding due to urban induced thunderstorms to the spread of toxic air contaminants within urban canyons. While recent efforts have yielded more detailed and realistic simulations of urban zone meteorological fields, additional work is required. Some remaining challenges are relevant for all mesoscale meteorological modeling efforts, while some are unique to urban domains. This paper reviews the key aspects of urban climate and discusses some challenges to modeling urban areas. These include turbulence formulations during stable and unstable conditions; nesting of urban boundary layer models within larger scale models and to canyon scale models; specification of urban surfaces and their boundary conditions, including use of satellite-derived land surface data; incorporation of observation canyon, roof top, and PBL data within urban models; linkages to air quality simulation models; and communication of results to urban planners and emergency responders. Examples will be presented from a variety of weather and air quality applications, including urban effects on thunderstorms, sea breeze fronts, and synoptic fronts.