The analysis of market structure and concentration measures for the Intermodal Freight Transport (IFT) market is important to avoid market failure and to find the areas for policy making to promote IFT market share. This analysis can be performed for separate segments, for example, the market for transshipment service or the market for main-haulage service. However, due to the multistage characteristic of IFT service, the segmental analysis gives an incomplete view of the IFT market at the network level. In a previous paper (Saeedi et al., 2017), we present the Intermodal Freight Transport Market Structure (IFTMS) model to conduct a network-based study of the IFTMS in which distinctive actors (i.e., pre/post haulage operators, terminals, rail/barge operators, transport chains, and corridors) are competing at different levels inside distinctive markets to deliver an integrated IFT service. There are two main challenges in the application of IFTMS model in real cases, for example, the European IFT network. First, the definition of the geographical and spatial border of the transshipment market areas is needed to determine which actors are potentially competing for a specific service demand. The second challenge is the lack of disaggregated data and the consistency of existing data in nodes (i.e., the transshipment areas) and links (i.e., the rail and barge operators). To cope with these challenges, we develop a four-step methodology in which a model-based approach is used to define the geographic boundaries of the transshipment submarkets and provide detailed and consistent data for market analysis. We also apply the IFTMS model to study the market structure of European intermodal network. Our analysis shows that the majority of transshipment markets as well as main-haulage markets are highly concentrated markets. The corridor markets – which include the IFT chains – are unconcentrated markets. Furthermore, the majority of corridors in the European Union are inside highly concentrated origin-destination markets.