Increasing interest in renewable fuels inspired a three-day workshop in Toronto in February 2008, entitled: The Scientific Foundation for Sustainable Forest Biomass Harvesting Guidelines and Policy. In this paper, we summarized the biodiversity-focused content of the workshop, including potential implications of intensification of biomass removal on biodiversity, knowledge gaps identified by workshop participants, and implications for policy development. Woody debris represents an important habitat resource for a wide variety of forest organisms, and the presence and continued supply of fresh to highly decayed dead wood represents a key concern in managed forest systems. A key challenge in sustainable forests management is to determine to what extent biomass harvests can increase fibre use while sustaining biodiversity, its functions, and the broad suite of ecosystem services that it provides. For knowledge-based planning and policy development, researchers must provide complex information to policy-makers and forest managers in a clear, effective way. In particular, full life-cycle analysis of intensive forest biomass harvesting taking into account environmental consequences is needed to inform sound evidence-based policy and decision-making. In the absence of complete scientific information, forest managers and decision-makers are well-advised to proceed with caution within a well-developed adaptive management framework.