The entry into force of the Nagoya Protocol of the Convention on Biological Diversity will lead to new legislation and regulations that could change international collaborative research in biology. This article suggests a new approach that researchers can use in negotiating international Access and Benefit Sharing agreements under the Protocol. Research on medicinal plants is used as a case study because it is a domain with many competing stakeholders involving non-commercial and commercial research, as well as national and international commercial markets. We propose a decision-based framework to aid all participants as they negotiate ABS agreements for non-commercial biodiversity research. Our proposed approach promotes transparency and builds trust, reflects the principles in the Convention on Biological Diversity, and respects and protects the interests of biodiversity rich developing countries. This approach is an alternative to often-used adversarial approaches.