The Baltic Institute of Finland contracted EFIS Centre to support the methodology development for a high-level interregional smart specialisation (S3) value chain mapping in the Baltic Sea Region (BSR). BSR was the first macro-region to adopt a common strategy, in 2009, the European Union Strategy for the Baltic Sea Region (EUSBSR). The BSR comprises eight countries: Denmark, Estonia, Finland, Germany, Latvia, Lithuania, Poland and Sweden. Norway, Belarus and Russia are also close collaborators with the BSR countries. The value chain mapping exercise is supporting the Interreg BSR Smart Specialisation Ecosystem ‘Platform’ project, which aims to build capacity across the macro-region for innovation-focused interregional collaboration. This study contributes to two key objectives: Provide analytical insights on value chains in a selected focus area and foster motivation for the mobilisation of BSR interregional effort in S3 collaboration; Provide an outline manual with key steps to take in undertaking a macro-regional value chain mapping exercise across any sector or domain targeted at BSR innovation/ S3 actors. The approach to high-level value chain mapping that was piloted for CBE is experimental. Due to the time and resource constraints underpinning the Interreg project the pilot analysis performed by EFIS Centre adopted a ‘fast-track’ approach. The main objective was to identify the current possibilities for carrying out such an exercise and the existing gaps in data coverage. The pilot exercise is intended to trigger further thinking and input from the BSR regions and innovation actors concerning additional market-led information which could be added to the mapping effort. This guidance manual draws lessons from the pilot exercise and provides an outline method for high-level value chain mapping, guiding the reader through the three main stages in order to enable reproduction of similar exercises in the future. The conclusions bring together overarching recommendations for the value chain methodology, with a focus on those aspects that may bring the highest value added to S3 policy making – both at regional and macro-regional levels.