This thesis aims to contribute to the policy debate on the complexity of passenger rail markets and to provide recommendations for the Dutch market. An extensive literature review has been conducted to identify the policy issues that must be discussed when dealing with passenger rail markets. These issues are structured in a theoretical framework to describe market structures and understand market complexity. The framework classifies the policy issues into three levels of decision-making, influenced by causal factors and resulting in system performance measured by three categories of indicators. The approach to passenger rail market analysis proposed in this thesis can be useful for researchers and policymakers to assess passenger rail markets in a structured way. The relevance of the policy issues was identified through a Delphi study involving 13 experts and stakeholders. As a result of the study, the role of different levels of government in market coordination, coordination of investments, timetables and incidents, and the level of transition costs were identified as key policy issues. An analysis of the Dutch market resulted in a recommendation to continue direct award to Nederlandse Spoorwegen on the main rail network. However, it is also recommended that Dutch policymakers prepare for the introduction of competition to strengthen their coordinating role and be ready for the eventuality of competition.