Many developing countries are currently in the process of designing regulatory systems that should make it possible to use the potential of genetically modified organisms (GMOs) for agricultural development, while at the same time managing the risks for food safety and the environment that are potentially associated with these technologies. In view of the considerable costs associated with biotechnology regulation and the scarcity of biosafety specialists, there are processes in various regions of the developing world to establish regional systems of biotechnology regulation. So far, there are major knowledge gaps as to how regional systems of biotechnology regulation can be designed to be effective and efficient and to fulfill principles of good governance, such as transparency, voice and accountability, control of corruption, and avoidance of special interest capture. There is a wide variety of possible regional approaches, which differ with regard to the level of centralization, the scope of a regional system, the types of regional institutions and processes, and the types of financing mechanisms. Based on the literature on environmental and fiscal federalism and transaction costs economics, the paper develops a conceptual framework for the assessment of regional systems of biotechnology regulation. The framework specifies design options and assessment criteria, and identifies major trade-offs as well as the factors affecting these trade-offs. The paper takes West Africa as an example to illustrate this framework and refers to the European Union for comparison. The paper concludes that involving regional experts, stakeholders and policy-makers into debates on the design of a regional regulatory system is an important strategy to fill knowledge gaps and arrive at conclusions regarding the trade-offs involved in regional biotechnology regulation. Key words: regional biotechnology regulation; regulatory federalism; transaction cost economics; West Africa; European Union