Federal and state transportation planners and others seeking to analyze transportation systems find few publicly available rail analysis models to estimate the operational costs and environmental impacts of rail movements. Moreover, data to populate such models and to test public policy considerations for evaluating public–private partnerships are generally difficult to obtain. This paper, a product of a study funded by Region 6 of the University Transportation Center Program, offers stakeholders the building blocks to develop an integrated rail analysis model capable of testing railway operational and capital investment changes. The paper also reviews the current state of rail modeling, examines selected rail models, and presents the findings of a preliminary intermodal rail costing model developed in the work.