Since the enactment of the America Invents Act, inter partes review has been a new pathway for challenging patents. This administrative proceeding at the Patent Trial and Appeal Board has had a pro-challenger bias. IPR proceedings apply a lower standard of proof than federal district courts, use the anti-patentee claim construction standard of broadest reasonable construction, and lack the Article III standing requirement of district court litigation. This Article explains how these differences create great uncertainty in pharmaceutical patents, and what could be done to restore the balance that was created in the Hatch-Waxman Act. Pharmaceutical patents have their own alternative litigation pathways with the Hatch-Waxman Act, passed by Congress over three decades ago, and the recent Biologics Price Competition and Innovation Act. Both balance between stimulating innovation from brand companies who hold patents and facilitating market entry from generic companies who challenge the patents. Hatch-Waxman and BPCIA litigation occur in the federal district courts, which have significantly lower patent invalidation rates than IPR proceedings. The Article argues that this uncertainty in patent rights will harm pharmaceutical innovation by decreasing incentives. Pharmaceutical companies will not spend the billions of dollars needed to research, develop, and bring a drug to market if patent validity in IPR proceedings is uncertain. In the end, the author proposes several reforms for Congress to enact that can reduce the disparities between IPR proceedings and Hatch-Waxman litigation so the balance between patent holders and patent challengers is restored.