Patentable subject matter in the United States is governed by 35 U.S.C. 101. The current patentable subject matter practice in the U.S. is very different from the corresponding practices by WIPO/Patent Cooperation Treaty and by the European Patent Office, and it is considered to be broader in general.

The US Constitution gives the Congress broad powers to decide what types of inventions should be patentable and what should not be, as long as patenting of these inventions "promotes the Progress of Science". Uncontroversially, patenting of research tools, scientific discoveries and scientific theories is excluded, since it would inhibit rather than "promote the Progress of Science".a. ABUSE OF RIGHTS OR LAW AS A LIMIT TO PATENT RIGHTS. AN ANALYSIS OF REACH-THROUGH ROYALTIES AS A FORM OF CONTRACTUAL EXPLOITATION OF RESEARCH-TOOLS PATENTS UNDER COLOMBIAN LAW. 2022. Rev Prop Inmater. 34, 137-62. N.C. Lopez. doi: 10.18601/16571959.n34.06. b. The ethics of access to patented biotech research tools from universities and other research institutions. 2018. Nat Biotechnol. 36/6, 495-9. K.J. Egelie, S.P. Strand, B. Johansen, B.K. Myskja. doi: 10.1038/nbt.4165. c3. The TRIPS Agreement and an Experimental Use Exception for 'Research Tools'. 2015. SSRN Electronic Journal. C. Dent. doi: 10.2139/ssrn.2626323. d. Analysis on Patentability of Research Tools. 2014. Law review. Z. We. e. Research Tools and the Hatch-Waxman Safe Harbor. 2014. Biotechnol Law Rep. 33/1, 21-6. D. Coggiobrian. doi: 10.1089/blr.2014.9997. f. Research Tool Patent and Its Justification. 2009. Journal of Industrial Property. 28/1-30. S. Yook.

However, besides research tools etc. there is another (and more controversial) question of whether some patent claims can be too broad and may pre-empt all uses of a particular discovery. The Alice-Mayo test discussed below aims to address this issue.

Since the enactment of the subject matter requirement ca. 1970, the interpretation of the statute changed multiple times. Although Section 101 of Title 35 U.S.C. reads:

and, thus, does not say what is patent-eligible and what is not, US courts felt that some inventions should not be subjected to patent monopoly at all (supposedly because certain claims may be too broad and may pre-empt all uses of a particular discovery), and used U.S.C. 101 as an excuse to enforce their own believes (and not of the US Congress). To quote the SCOTUS in Myriad: "Without this exception, there would be considerable danger that the grant of patents would ‘tie up’ the use of such tools and thereby ‘inhibit future innovation premised upon them.’"

The two particularly contentious areas, with numerous reversals of prior legislative and judicial decisions, have been computer-based (see Software patents under United States patent law) and biological inventions.Prometheus and Bilski: Pushing the Bounds of Patentable Subject Matter in Medical Diagnostic Techniques with the Machine-or-Transformation Test. 2010. Am J Law Med. 36/4, 619–51. S. Pessagno. doi: 10.1177/009885881003600404. While these two areas present different types of challenges:Biotech Patent Eligibility: A New Hope. Columbia Business Law Review. 2017/3, 1157–999. E. Kim. doi: 10.7916/cblr.v2017i3.1729.

(a) the problem with biological inventions is where the discovery of Nature's work ends and where a human invention begins, i.e. patent monopoly should not encompass a "natural phenomenon or a law of nature".

(b) the problem with the software inventions (such as “mathematical algorithms, including those executed on a generic computer,... [and] some fundamental economic and conventional business practices")Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2110–11 (2013) is that the scope of such claims is incommensurably broad compared to their contribution to "the Progress of Science" (quid pro quo),

the US Courts rejected early attempts to develop different set of rules for the two challenges and instead tried to find a common approach to these, as well to potential other subject matter eligibility challenges in the future. One amicus curiae plainly called this approach "one attempt [at] a universal framework via amorphous and misguided patent eligibility requirements."Rethinking Patent Eligibility for the Modern Scientific Age. 2014. SSRN Electronic Journal. P.S. Menell, J.A. Lefstin. doi: 10.2139/ssrn.2402776.

Nevertheless, this approach, known as Alice- Mayo framework, was developed by the SCOTUS in 2012–2014, and has been used by the USPTO and by US courts since. The unified Alice-Mayo approach to subject matter eligibility requires (1) the newly discovered Law of Nature or mathematical formula to be assumed as known, (2) an additional "inventive concept", that limits the application of (1) to a specific and non-trivial use.

There is an important relationship between patent eligibility and non-obviousness tests in the US patent law. The non-obviousness criterion can be easily met, if a claim is based on a discovery of new natural phenomenon/principle/law. In the patentable subject matter analysis, however, this "discovery" is assumed to be prior art, and an "additional inventive concept" must be present in the claim.Genetic Technologies Ltd. v. Merial LLC: Gene-Based Assays in the Wake of Mayo. 2016. Biotechnol Law Rep. 35/3, 89–92. M. Sanzo. doi: 10.1089/blr.2016.29015.ms.

Although the details are discussed below, the net result as of year 2023 can be summarized as follows:

Things (including living organisms and nucleic acids) found in nature are not patent-eligible (Funk Bros. Seed Co. v. Kalo Inoculant Co.) even, when isolated from their natural environment (e.g. a protein-encoding gene from a chromosome), but things (even alive) "made by man" may be (Diamond v. Chakrabarty, Association for Molecular Pathology v. Myriad Genetics, Inc.), provided that they are different in a useful manner from their natural predecessor(s).

In the case of computer-implemented methods, the algorithms (even new and non-obvious) per se are not patentable (Gottschalk v. Benson, Parker v. Flook), but their new and useful applications may be patentable (Diamond v. Diehr).Alice at Six: Patent Eligibility Comes of Age. 2021. Chi-Kent J Intell Prop. 20/64. M.A. Perry, J.S. Chung.

The Mayo, Myriad and Ariosa v. Sequenom patents are similar in being based on a "discovery" of a natural phenomenon or a mathematical law (as in Gottschalk v. Benson), that assures the novelty and non-obviousness of the patent claims. Yet, when this "discovery" is assumed to be a prior art (as the Mayo-Alice test requires), a patentable claim must have an additional "inventive concept" or "inventive application". The purpose of this requirement is to prevent monopolization of all (or many) uses of the "discovery". One legal commentator wrote, that the additional "inventive concept" requirement is reminiscent of the inventive step requirement of the Patent Cooperation Treaty and of European Patent Convention, and that some of US patent rejected due "subject matter eligibility" had their foreign counterparts rejected for the lack of inventive step.The Inventive Concept in Alice Corp. v. CLS Bank Int'l. 2014. Int Rev Intellect Prop Compet Law. 45/8, 865–7. D.L. Burk. doi: 10.1007/s40319-014-0285-9; 10.31235/osf.io/67knf

Historic development The legislative and judicial history of the later is illustrated in the figure below:

The subject-matter exception to patenting mathematical formulas and algorithms arose out of three Supreme Court cases commonly referred to as the "patent-eligibility trilogy" between 1972 and 1981: Gottschalk v. Benson, Parker v. Flook, and Diamond v. Diehr. These three cases can be share a common view, that when the only new element in a claim is a natural law/phenomenon or an abstract idea, the claim is patent-ineligible. As Nielson and Morse said, and Flook reaffirmed, the natural law/phenomenon must be treated as if it is a prior art. An additional "inventive implementation" is required in a claim to make patent-eligible.Chi-Kent J Intell Prop. 20/64. M.A. Perry, J.S. Chung. (2021). Alice at Six: Patent Eligibility Comes of Age

1852 Le Roy v. Tatham This rarely cited case can be considered as the earliest example of patentable subject matter controversy decided by the SCOTUS. In this case the inventors discovered a new property of lead metal, which turned out be useful in making lead pipes. However, the claimed apparatus was essentially the same as old known lead pipe making machines. The 5-judge majority decided, that the patent essentially claimed the discovery per se, and invalidated the patent: a principle is not patentable. A principle, in the abstract, is a fundamental truth; an original cause; a motive; these cannot be patented, as no one can claim in either of them an exclusive right.Le Roy v. Tatham, 55 U.S. 156, 175 (1852) A 3-judge minority stated, that:

The minority held that "the invention in itself was not in discovering the abstract principle, which is open to all, but in applying the principle to a useful object."Echoes from the Past: How the Federal Circuit Continues to Struggle with Patentable Subject Matter Post-Bilski. 2012. Missouri law review. 77/2, 10. J. Thruston. Similar judicial philosophy was adopted by Federal Circuit Judge Pauline Newman in Ariosa v. Sequenom, but this approach was firmly rejected by the SCOTUS in Mayo Collaborative Services v. Prometheus Laboratories, Inc. and it is not the controlling law in the USA.

1853 O'Reilly v. Morse In this case, Samuel Morse applied for a patent with a claim on "the use of the motive power of the electric or galvanic current, which I call electro-magnetism, however developed for marking or printing intelligible characters, signs, or letters, at any distances". While other more narrow claims were allowed, this broad claim was invalidated by, because such a broad claim would likely hinder rather than "promote the Progress of Science", as the patent clause of the US Constitution requires.

1948 Funk Bros. Seed Co. v. Kalo Inoculant Co. This SCOTUS decision is considered as the forebear of the "inventive application" requirement as a test for patent eligibility.

The patent in question claimed a combination of several bacterial strains, which help bean plants with nitrogen fixation. These different bacteria surprisingly did not inhibit each other, thus displaying a form of symbiosis instead. The problem with this "invention" was that it was not "made by man", but rather discovered in Nature. The majority opinion stated:

1972 Gottschalk v. Benson The invention in this case was a method of programming a general-purpose digital computer using an algorithm to convert binary-coded decimal numbers into pure binary numbers. Although, the method was previously unknown and non-obvious, the Supreme Court found that the process in Benson was unpatentable since the invention, an algorithm, was no more than abstract mathematics. More generally, the Court noted that phenomena of nature, mental processes and abstract intellectual concepts were not patentable, since they were the basic tools of scientific and technological work. However, new and useful inventions derived from such discoveries are patentable.