Because of growing concerns about the future environmental impact of passenger travel, modal energy efficiency is becoming increasingly important when benefits and costs of transportation system investment are evaluated. Because passenger rail systems are often cited as being relatively more energy efficient than other modes, reduced environmental impact is one justification for investment in new commuter rail projects. It is important that studies of purported environmental benefits analyze the energy efficiency of passenger rail systems and competing modes accurately and fairly by clearly defining the flow of energy through each transportation system. Furthermore, operational practices and constraints of the railway environment can complicate the analysis of energy efficiency; this complication makes it important to choose metrics that accurately describe the situation. This research identifies and describes four methods for analyzing the energy efficiency of passenger rail systems. Each method applies to a different system within the energy flow path. The combined methods are used to analyze the energy efficiency of 25 commuter rail systems in the United States. The results of each energy efficiency calculation method are then compared to illustrate how the relative attractiveness of each system can change on the basis of the selected analysis approach. By better understanding the challenges of conducting energy efficiency analyses involving different energy sources and fair comparison methods, researchers and policy makers can make informed decisions concerning the most appropriate method of analysis for drawing accurate comparisons between rail technologies and competing modes.