The relationship between intellectual property rights (IPRs) and investment treaty arbitration is a relatively new phenomenon. One reason is that the intellectual property system has been designed, implemented and enforced on the national level. A state may use the World Trade Organization dispute settlement mechanism for the clarification of an Agreement on Trade- Related Aspects of Intellectual Property Rights (TRIPS) provision. Alternatively, parties can resolve disputes either on the national level or through alternative dispute resolution, mainly arbitration and mediation. Despite the traditional practice, investors have brought forward intellectual property-related investor-state dispute settlement disputes in Philip Morris v. Uruguay and Eli Lilly v. Canada, which created opportunities for possible IPR litigation in the future. This paper critically examines the two disputes and broadly analyzes the important findings of these cases. The paper analyzes the arguments of the parties and the tribunal conclusions to show potential implications and challenges which these disputes might bring to the intellectual property system.