Biodiversity offsets are an increasingly popular yet controversial tool in conservation. Their popularity lies in their potential to meet the objectives of biodiversity conservation and of economic development in tandem; the controversy lies in the need to accept ecological losses in return for uncertain gains. The offsetting approach is being widely adopted, even though its methodologies and the overriding conceptual framework are still under development. This review of biodiversity offsetting evaluates implementation to date and synthesizes outstanding theoretical and practical problems. We begin by outlining the criteria that make biodiversity offsets unique and then explore the suite of conceptual challenges arising from these criteria and indicate potential design solutions. We find that biodiversity offset schemes have been inconsistent in meeting conservation objectives because of the challenge of ensuring full compliance and effective monitoring and because of conceptual flaws in the approach itself. Evidence to support this conclusion comes primarily from developed countries, although offsets are increasingly being implemented in the developing world. We are at a critical stage: biodiversity offsets risk becoming responses to immediate development and conservation needs without an overriding conceptual framework to provide guidance and evaluation criteria. We clarify the meaning of the term biodiversity offset and propose a framework that integrates the consideration of theoretical and practical challenges in the offset process. We also propose a research agenda for specific topics around metrics, baselines and uncertainty.