Using cluster analysis, a total of 605 vents in San Francisco Volcanic Field are studied over an area of approximately 5000km2. Application of alignment analysis techniques, including the two-point azimuth analysis and Hough transform analysis, demonstrates that cinder cones are aligned along common orientations within larger clusters. These alignments consist of 9-10 cinder cones, are 20-38 km long, and are regional features. The vent alignments indicate the presence of geological features along which magma ascended more readily than elsewhere. The NE-trending Mesa Butte and Oak Creek Canyon-Doney fault systems seem to control the intermediate to silicic centers which are on the intersection of these fault systems with Cataract Creek fault system and affect the development of cinder cone alignments. Geological maps and geophysical surveys indicate that most vent alignments are parallel or subparallel to these large scale fault systems. This suggests that vent alignment patterns are controlled by regional structures.