The core concepts, or threads, of Biosystems Engineering (BSEN) are variously understood by those within the discipline, but have never been unequivocally defined due to its early stage of development. This makes communication and teaching difficult compared to other well established engineering subjects. Biosystems Engineering is a field of Engineering which integrates engineering science and design with applied biological, environmental and agricultural sciences. It represents an evolution of the Agricultural Engineering discipline applied to all living organisms not including biomedical applications. The basic key element for the emerging EU Biosystems Engineering program of studies is to ensure that it offers essential minimum fundamental engineering knowledge and competences. A core curriculum developed by Erasmus Thematic Networks is used as benchmark for Agricultural and Biosystems Engineering studies in Europe. The common basis of the core curriculum for the discipline across the Atlantic, including a minimum of competences comprising the Biosystems Engineering core competencies, has been defined by an Atlantis project, but this needs to be taken further by defining the threads linking courses together. This paper presents a structured approach to define the Threads of BSEN. The definition of the mid-level competences and the associated learning outcomes has been one of the objectives of the Atlantis programme TABE.NET. The mid-level competences and learning outcomes for each of six modules of BSEN are defined while the domain-specific knowledge to be acquired for each outcome is proposed. Once the proposed definitions are adopted, these threads will be available for global development of the BSEN.