The Witherspoon Institute was founded in 2003 by, among others, Princeton University professor and noted conservative Robert P. George, Luis Tellez, and others involved with the James Madison Program in American Ideals and Institutions. Named after John Witherspoon, one of the signers of the United States Declaration of Independence, the institute's fellows include Chen Guangcheng, Harold James, John Joseph Haldane, and James R. Stoner, Jr.
The Witherspoon Institute opposes same-sex marriage and deals with embryonic stem cell research, constitutional law, and globalization. In 2003, it organized a conference on religion in modern societies. In 2006, Republican Senator Sam Brownback cited a Witherspoon document called Marriage and the Public Good: Ten Principles in a debate over a constitutional amendment against same-sex marriage. It held a conference about pornography named The Social Costs of Pornography at Princeton University in December 2008.
Financially independent from Princeton University, its donors have included the Bradley Foundation, the John M. Olin Foundation, the John Templeton Foundation, and the Lee and Ramona Bass Foundation.
The Witherspoon Institute also provides educational opportunities to high school students, undergraduate students, graduate students, and young faculty members. Most of these seminars focus on natural law philosophy and its applications in contemporary fields such as political theory, bioethics, and law.
On October 2, 2013, the Witherspoon Institute announced the appointment of Chinese lawyer and human rights activist Chen Guangcheng as Distinguished Senior Fellow in Human Rights at the Witherspoon Institute, as well as Visiting Fellow of the Institute for Policy Research and Catholic Studies at the Catholic University of America, and Senior Distinguished Advisor to the Lantos Foundation for Human Rights and Justice. In an interview, Luis Tellez, President of the Witherspoon Institute, told Reuters: "We're not asking him to do anything specific... The main point is he's a truth teller, he tries to tell the truth as he sees it." Tellez said that he expects Chen to continue his advocacy for human rights in China in his new appointment, which is set to last for the next three years.
On October 16, 2013, Chen made his first public appearance as a fellow of Witherspoon. He delivered a public lecture at Princeton University entitled "China and the World in the 21st Century: The Next Human Rights Revolution," co-sponsored by the Witherspoon Institute and the James Madison Program in American Ideals and Institutions. The text of Chen's speech, translated into English, was then published online. In the speech, Chen called on the American people to support the Chinese people by fighting against the Communist government of China. Chen asserted that even small actions undertaken in defense of human rights can have a large impact, because “Every person has infinite strength. Every action has an important impact. We must believe in the value of our own actions.”
In 2012, the Witherspoon Institute drew public attention for having funded a controversial study—called the "New Family Structures Study" (NFSS)—concerning LGBT parenting, conducted by Mark Regnerus, an associate professor of sociology at the University of Texas at Austin. The study was criticized by major professional scientific institutions and associations, as well as other sociologists at the University of Texas. Documents from the University of Texas at Austin indicate that Regnerus, was provided with guidance by the Institute, requested payment authorizations, for assistance in data analysis, to William Bradford Wilcox, associate professor of sociology at the University of Virginia, a member of the James Madison Society at Princeton University, the director of the National Marriage Project at the University of Virginia, and fellow (at that time) of the Witherspoon Institute. Critics argue that these documents show direct involvement in the study by the Witherspoon Institute. Furthermore, the methodology of the study has received criticism The University of Texas, conducted an inquiry into the publication and declined to conduct a personal investigation in keeping with its policy that "ordinary errors, good faith differences in interpretations or judgments of data, scholarly or political disagreements, good faith personal or professional opinions, or private moral or ethical behavior or views are not misconduct." Nevertheless, the University of Texas sociology department acknowledged the Regnerus study was "fundamentally flawed on conceptual and methodological grounds and that findings from Dr. Regnerus’ work have been cited inappropriately in efforts to diminish the civil rights and legitimacy of LBGTQ partners and their families." 
The conclusions asserted by the study relied on a number of methodological flaws. A review by the American Medical Organization noting that :
... The data does not show whether the perceived romantic relationship ever in fact occurred; nor whether the parent self-identified as gay or lesbian; nor whether the same sex relationship was continuous, episodic, or one-time only; nor whether the individual in these categories was actually raised by a homosexual parent (children of gay fathers are often raised by their heterosexual mothers following divorce), much less a parent in a long-term relationship with a same-sex partner. Indeed, most of the participants in these groups spent very little, if any, time being raised by a “same-sex couple.”
In 2012, Darren Sherkat, professor of sociology at Southern Illinois University and a member of the editorial board of Social Science Research was asked by the journal's editor to audit the peer-review process that led to publication of the Regnerus study. In the November 2012 issue of Social Science Research Sherkat published the conclusion of his audit that, although established procedure was followed insofar as the peer reviewers were of the journal's customary standing, they were improperly affiliated with Regnerus and the study's data collection and analysis methods were badly flawed, rendering it unsuitable for publication. In an interview with the Southern Poverty Law Center, Sherkat described the study as being "deeply methodologically flawed and a peer-review process that failed to identify significant problems." Sherkat also asserted that the study was riddled with technical flaws. Sherkat said he thought that Regnerus, a conservative Christian, had "disgraced" himself by drawing misleading conclusions from poor research.
In Regnerus' defense his former doctoral advisor, sociologist Christian Smith, has argued that, while "his article is not perfect," nevertheless "it is no scientifically worse than what is routinely published in sociology journals." Smith, who says he is not a conservative, nevertheless described the response to the Regnerus study as a "witch hunt," adding that "Regnerus published ideologically unpopular research results on the contentious matter of same-sex relationships. And now he is being made to pay."
We do not think that [the Regnerus study and others] settle the nation’s ongoing debate about gay parenting, same-sex marriage, and the welfare of children. In fact, research on same-sex parenting based on nationally representative samples is still in its infancy. But we think that the Regnerus study, which is one of the first to rely on a large, random, and representative sample of children from parents who have experienced same-sex relationships, has helped to inform the ongoing scholarly and public conversation about same-sex families in America.
Multiple amicus curiae briefs to federal courts including United States Supreme Court by major health and academic organizations including the American Sociological Association, American Academy of Pediatrics and American Medical Association have criticized the methodology and conclusions reached by the NFSS as lacking scientific validity and being unsupported by the study's own data. A review by the American Sociological Association noting "The Regnerus study offers no basis for conclusions about same-sex parents" Writing to the United States Ninth Circuit Court of Appeals the American Medical Association cited the study's poor methodology to explain why "the Regnerus study sheds no light on the parenting of stable, committed same-sex couples – as Regnerus himself acknowledges," and reaffirmed that "the conclusions by the leading associations of experts in this area reflect a consensus that children raised by lesbian or gay parents do not differ in any important respects from those raised by heterosexual parents."
- Religious Freedom: Why Now? Defending an Embattled Human Right (2012)
- Embryo: A Defense of Human Life
- The Social Costs of Pornography: A Collection of Papers (2010)
- The Social Costs of Pornography: A Statement of Findings and Recommendations (2010)
- Rethinking Business Management: Examining the Foundations of Business Education (2008)
- Marriage and the Public Good: Ten Principles (First edition, 2006; Second edition, 2008)
- The Meaning of Marriage: Family, State, Market, And Morals
- Official website: Mission
- Deborah Yaffe, 'A conservative think tank with many Princeton ties', in Princeton Alumni Weekly, July 16, 2008
- David D. Kirkpatrick, The Conservative-Christian Big Thinker, The New York Times, December 16, 2009
- Robert P. George & Jean Bethke Elshtain, The Meaning of Marriage, Scepter Publishers, p. vii
- Allen, Jonathan (2013-11-25). "Friends Like These: How a Famed Chinese Dissident Got Caught Up in America's Culture Wars". New York: Reuters.
- Official website: Fellows
- Roger Scruton, A political philosophy, Continuum International Publishing Group, 2006, p. 210
- Public Discourse website
- Catholic News Agency article about Witherspoon Seminars
- National Review article on Witherspoon Seminars
- First Things article on Natural Law and Public Affairs Seminar
- Steve Kolowich, Is the Research All Right?, Inside Higher Ed, July 13, 2012
- NFSS FIOA Amato Wilcox
- Resnick, Sofia. "Goal of UT parenting study was to influence SCOTUS decisions on gay marriage, docs show". The American Independent. Retrieved 31 October 2013.
- Gates, Gary & al. "Letter to the editors and advisory editors of Social Science Research". Social Science Research. Retrieved 31 October 2013.
- "University of Texas at Austin Completes Inquiry into Allegations of Scientific Misconduct". University of Texas at Austin. Aug 29, 2012. Retrieved December 3, 2012.
- "Statement from the Chair regarding Professor Regnerus". University of Texas at Austin. Mar 3, 2014.
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- Sherkat, Darren (November 2012). "The editorial process and politicized scholarship: Monday morning editorial quarterbacking and a call for scientific vigilance". Social Science Research 41 (6). Retrieved 2 November 2013.
- "Suspect 'Science,'" Intelligence Report, Summer 2013, Issue 150, Southern Poverty Law Center, splcenter.org, accessed 29 May 2013.
- "An Academic Auto-da-Fé: A sociologist whose data find fault with same-sex relationships is savaged by the progressive orthodoxy" Chronicle of Higher Education, July 23, 2012 accessed 7 June 2013.
- Johnson, Byron, & al. (June 20, 2012). "A Social Scientific Response to the Regnerus Controversy". Retrieved 24 April 2014.
- "BRIEF OF AMICUS CURIAE AMERICAN SOCIOLOGICAL ASSOCIATION IN SUPPORT OF RESPONDENT KRISTIN M. PERRY AND RESPONDENT EDITH SCHLAIN WINDSOR" American Sociological Association, February 28, 2013 accessed 7 June 2013.
- " http://www.huffingtonpost.com/john-becker/supreme-court-american-sociological-association-gay-parents_b_2783523.html