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Purpose – The purpose of this paper is to identify the most significant uncertainties for bioenergy applications, in order to identify factors determining the success of introducing bioenergy into the current energy system. Design/methodology/approach – A framework is built for identifying the most significant uncertainties based on studies exploring the positive potentials as well as possible negative effects of bioenergy. The framework is applied to explore uncertainties of bioenergy-based transport fuels and heat and power generation through two real life case studies. Findings – The results indicate that the most significant uncertainties are environmental and economic. Bioenergy applications have potential to mitigate climate change, but also come with negative environmental effects. Case studies show that operations in developing nations contain higher political/institutional and social uncertainty than those in developed countries, due to weaker regulations and enforcement. Research limitations/implications – The paper is part of an on-going research project. Results will be verified with stakeholder interviews and analysis. Further institutional analysis of the country settings is necessary. Practical implications – The use of a feedstock with high environmental, social and institutional uncertainties will lower public acceptance. Acting in accordance to the law is not sufficient to ensure sustainability and additional, voluntary measures should be undertaken. Originality/value – The paper identifies the most significant uncertainties for bioenergy. Uncertainties from social acceptance and institutional settings are higher in developing countries and acceptability requires more than following regulations.

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