In 2011 the Global Bioenergy Partnership (GBEP) released a set of indicators for sustainable bioenergy. However, two important issues still remain unresolved. One of them is the definition of "sustainability", and the other is the lack of a holistic assessment tool for drawing conclusions from the indicators. The aim of this paper is to provide clarification on the concept of sustainability in the context of the GBEP indicators, and to develop a holistic assessment tool for assessing the sustainability of bioenergy programmes. The GBEP indicators are diverse in terms of "what to measure", and some of them are not sufficiently directly related to the concept of sustainability. This makes the indicators ambiguous regarding to sustainability assessment. This study identifies whether the GBEP indicators are concerned with strong or weak sustainability, and develops a tool based on Multi Criteria Analysis (MCA) which can be used for assessing sustainability of bio-energy programmes using the GBEP indicators. The tool is demonstrated in an example for assessing the sustainability of biofuel production in a case study of Kyoto. We found that the biodiesel production in Kyoto performs well on the environmental pillar, but badly on the economic pillar, and based on the weights applied in this study the overall sustainability is better than diesel fuel. The holistic assessment tool provides practical information to policymakers on both ex-ante and ex-post policy evaluations. (C) 2014 Elsevier Ltd. All rights reserved.