This research puts forth an examination of the relationship between municipal planning and short line freight railroads. Methodologically, it employs a content analysis framework that explores local master plans and zoning bylaws for the presence of concepts relevant to short line railroads. A historically omitted topic, the railroads are found to be frequently omitted from plans, often conflicting with civic and recreational interests despite their increasingly efficient ability, economic and environmental, to service numerous industries. Zoning bylaws show a disfavor to these entities, and at times may exceed their authority. Moreover, they may create physical and legal limitations to new, rail-sustained industry, as well as the rehabilitation of former industrial clusters. Findings related to regulatory preemption, transportation and land use policy, corridor conversion, and shifting land use patterns are presented. Consequentially, daunting implications may resonate for both the railroad and municipalities. Recommendations encompass municipal, regional, and state policy, as well as opportunities for multi-agency collaboration, economic development initiatives, and revised regulatory structures.