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In order to understand the climate effects of a bioenergy system, a comparison between the bioenergy system and a reference system is required. The reference system describes the situation that occurs in the absence of the bioenergy system with respect to the use of land, energy, and materials. The importance of reference systems is discussed in the literature but guidance on choosing suitable reference systems for assessing climate effects of bioenergy is limited. The reference system should align with the purpose of the study. Transparency of reference system assumptions is essential for proper interpretation of bioenergy assessments. This paper presents guidance for selecting suitable reference systems. Particular attention is given to choosing the land reference. If the goal is to study the climate effects of bioenergy as a part of total anthropogenic activity the reference system should illustrate what is expected …