A novel, nonobvious Discovery Tool and its use can be the subject of valid patent claims, but patent claims that reach through to cover as-of-yet-undiscovered drug products generally fail to meet the written description and enablement requirements of 35 U.S.C. § 112. Notwithstanding the Supreme Court’s broad reading of the scope of the statutory exemption to infringement—under 35 U.S.C. § 271(e)(1)—in Merck v. Integra, and the occasionally misapplied common law experimental use exception, valid claims to Discovery Tools and their use are enforceable against unauthorized users. This article analyzes the legality of one form of compensation occasionally sought by Discovery Tool inventors as consideration for the grant of a license to the use of their patented tools: the “reach-through” royalty paid on the sale of a product that is identified by a licensee using a patented Discovery Tool, but is not itself covered by the inventor’s tool patent. In addition, this article reviews judicial remedies in patent infringement cases that reach through the infringed patent to burden products and activities of the infringer that are not covered by the infringed patent—remedies that are analogous to a negotiated contractual reach-through royalty obligation. The article concludes that reach-through royalty arrangements between willing licensors and licensees are permissible under U.S. Supreme Court precedent, despite potential patent misuse challenges, and represent a viable method by which the free market for patented Discovery Tools may adequately reward the tool inventor.