Courts and administrative agencies have clashed over issues raised by gene patenting. In this article, the authors first offer a synopsis of the historical problems that the patent system has encountered in dealing with innovations such as those flowing from the Human Genome Project. The authors then discuss the prohibitions on the patenting of naturally occurring phenomena and the patenting of preexisting products that have merely been isolated, purified, or otherwise altered in some way. The authors then analyze the doctrine as it relates to the 1952 Patent Act. The authors go on to discuss the differences between biochemical innovations and other types of innovations and present the "substantial transformation test" as a bridge between proper patent doctrine and omissions in the current Patent Act. The authors demonstrate how the test can be used to distinguish new biotechnology inventions from unpatentable discoveries of natural phenomena.