Prompt and affordable access to essential medicines is a component of almost all domestic and global public health models. As is now well known, the availability and costs of both brand and generic drugs is a function of traditional patent law incentives. Less known, however, is that generic entry is controlled increasingly through an emerging form of global intellectual property law referred to as “linkage regulations.” Linkage regulations tie generic drug approval, and thus access to essential medications, to existing drug patents through potentially long and costly litigation. The linkage regime is in the process of rapidly spreading worldwide through international free trade agreements. Even so, very little is known about how the regulations work in developed nations let alone how they impact on public health systems across international borders. The authors constitute a network of eleven health policy experts and practicing lawyers in nine countries including those with mature linkage regulations, those with new regulations, those without regulations but with practices that parallel linkage, and those where regulations are currently subject to intense public debate and litigation. Here, we propose a novel structure-function framework to conduct acomparative legal analysis of global pharmaceutical linkage, with the aim of obtaining critical information about the costs and benefits of tying pharmaceutical innovation and generic drug availability to drug patenting. A major goal of the research is to investigate the structural and functional aspects of global linkage regulations as they relate to drug availability, costs and expenditures on the one hand and incentives for innovation and protection of rights on the other. The structural and functional aspects we discuss here include: assessment in each jurisdiction of the original policy intent underpinning linkage; the manner in which public health policy and economic policy is perceived by governments and the courts to converge or diverge through linkage; the specific legal checks and balances designed specifically to maintain balance between the interests of brand and generic firms; the growing expansion of linkage beyond the drug approval-drug patenting nexus to encompass drug pricing and reimbursement; and the role of empirical studies to establish the legal legitimacy of linkage regulations. A second major goal of our work is to assist domestic and global governments and legal systems working with linkage regimes to balance the production of new and innovative drugs with timely generic entry, and thus to lower public health costs and increase access to essential medicines.