The aim of this paper is to present a survey of recent optimization models for the most commonly studied rail transportation problems. For each group of problems, we propose a classification of models and describe their important characteristics by focusing on model structure and algorithmic aspects. The review mainly concentrates on routing and scheduling problems since they represent the most important portion of the planning activities performed by railways. Routing models surveyed concern the operating policies for freight transportation and railcar fleet management, whereas scheduling models address the dispatching of trains and the assignment of locomotives and cars. A brief discussion of analytical yard and line models is also presented. The emphasis is on recent contributions but several older yet important works are also cited.