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Geographic information systems (GIS) are having tremendous impacts on many scientific and application domains. The traditional subfield of spatial analysis is witnessing a major resurgence and enhancement due to GIS and geographical information science (GISci), an interdisciplinary field focusing on the theory and methodology underlying GIS software. The interdisciplinary field of geographic information systems for transportation (GIS‐T) has emerged to focus on the role of GIS in transportaton analysis and planning. This paper suggests the benefits of closer linkages between spatial analysis, GISci, and transportation through a focused review of spatial analytical issues and their potential contributions to GIS‐T. Specifically, this paper reviews the following issues: (i) modifiable areal units; (ii) boundary problems and spatial sampling; (iii) spatial dependence and spatial heterogeneity; and (iv) alternative …