There are many different interpretations of creation stories in Abrahamic religions in which God creates people "male and female". This is sometimes interpreted as a divine mandate against challenging the gender binary and also for challenging the gender binary.
In the Baha'i Faith, transgender people can gain recognition in their gender if they have medically transitioned under the direction of medical professionals and if they have sex reassignment surgery (SRS). After SRS, they are considered transitioned and may have a Baha'i marriage.
The New Testament presents eunuchs (Greek eunochos, similar to Hebrew saris) as acceptable candidates for evangelism and baptism, as demonstrated in the account of the conversion of an Ethiopian eunuch. While answering questions about marriage and divorce, Jesus says that "there are eunuchs who have been so from birth, and there are eunuchs who have been made eunuchs by others, and there are eunuchs who have made themselves eunuchs for the sake of the kingdom of heaven." Discussion has occurred about the significance of the selection of the Ethiopian eunuch as being an early gentile convert to Christianity: the inclusion of a eunuch, representing a sexual minority, in the context of the time.
Some Christian denominations accept transgender people as members and clergy:
- In 2003, the United Church of Christ General Synod called for full inclusion of transgender persons.
- In 2005, Sarah Jones became the first openly transgender person to be ordained by the Church of England as a priest: the first transperson to minister in the Church of England was Carol Stone, who had been ordained in 1978 and transitioned in 2000.
- In 2008, the United Methodist Church Judicial Council ruled that openly transgender pastor Drew Phoenix could keep his position. At the UMC General Conference the same year, several petitions that would have forbidden transgender clergy and added anti-transgender language to the Book of Discipline were rejected. In 2017, the United Methodist Church commissioned its first non-binary clergy member, a transgender non-binary deacon named M Barclay. Also, Joy Everingham was the Methodist Church in Great Britain's first openly transgender minister.
- In 2012, the Episcopal Church in the United States approved a change to their nondiscrimination canons to include gender identity and expression.
- In 2013, Shannon Kearns became the first openly transgender person ordained by the North American Old Catholic Church. He was ordained in Minneapolis.
- In 2014, Megan Rohrer became the first openly transgender leader of a Lutheran congregation (specifically, Grace Evangelical Lutheran Church of San Francisco.) 
- In 2017, the General Synod of the Church of England passed a motion stating, "That this Synod, recognising the need for transgender people to be welcomed and affirmed in their parish church, call on the House of Bishops to consider whether some nationally commended liturgical materials might be prepared to mark a person's gender transition."
In contrast, a 2000 document from the Catholic Congregation for the Doctrine of the Faith concludes that the sex-change procedures do not change a person's gender in the eyes of the Church. "The key point", that document states, "is that the transsexual surgical operation is so superficial and external that it does not change the personality. If the person was a male, he remains male. If she was female, she remains female." The document also concludes that a "sex-change" operation could be morally acceptable in certain extreme cases, but that in any case transgender people cannot validly marry. Pope Benedict XVI denounced gender studies, warning that it blurs the distinction between male and female and could thus lead to the "self-destruction" of the human race. He warned against the manipulation that takes place in national and international forums when the term "gender" is altered. "What is often expressed and understood by the term 'gender,' is definitively resolved in the self-emancipation of the human being from creation and the Creator", he warned. "Man wants to create himself, and to decide always and exclusively on his own about what concerns him." The Pontiff said this is humanity living "against truth, against the creating Spirit". As well, in 2015, the Vatican declared that transgender Catholics cannot become godparents, stating in response to a transgender man's query that transgender status "reveals in a public way an attitude opposite to the moral imperative of solving the problem of sexual identity according to the truth of one's own sexuality" and that, "[t]herefore it is evident that this person does not possess the requirement of leading a life according to the faith and in the position of godfather and is therefore unable to be admitted to the position of godfather or godmother." Catholics, nevertheless, have held a range of positions regarding transgender issues. Theologian James Whitehead, for instance, has said, “The kind of transition that trans people are talking about is very similar to the journey of faith through darkness and desert that people have been making for thousands of years.” The Roman Catholic Church has been involved in the outreach to LBGT community for several years and continues doing so in a variety of ways such as through Franciscan urban outreach centers, namely, the "Open Hearts" outreach in Hartford, CT.
In 2006, Albert Mohler, then president of the Southern Baptist Theological Seminary, said "Only God has the right to determine gender", adding, "any attempt to alter that creation is an act of rebellion against God." He also stated, "Christians are obligated to find our definitions … in the Bible. What the activists want to call 'sex-reassignment surgery' must be seen as a form of bodily mutilation rather than gender correction. The chromosomes will continue to tell the story...Gender is not under our control after all. When a nation's moral rebellion comes down to this level of confusion, we are already in big trouble. A society that can't distinguish between men and women is not likely to find moral clarity in any other area of life." In 2014, the Southern Baptist Convention approved a resolution at its annual meeting stating that "God's design was the creation of two distinct and complementary sexes, male and female" and that "gender identity is determined by biological sex, not by one's self-perception". Furthermore, the resolution opposes hormone therapy, transition-related care, and anything else that would "alter one's bodily identity", as well as opposing government efforts to "validate transgender identity as morally praiseworthy". Instead, the resolution asks transgender people to "trust in Christ and to experience renewal in the Gospel".
Unitarian Universalism, a liberal religion with roots in liberal Christianity, became the first denomination to accept openly transgender people as full members with eligibility to become clergy (in 1979), and the first to open an Office of Bisexual, Gay, Lesbian, and Transgender Concerns (in 1973). In 1988 the first openly transgender person was ordained by the Unitarian Universalist Association. In 2002 Rev. Sean Dennison became the first openly transgender person in the Unitarian Universalist ministry called to serve a congregation; he was called to South Valley UU Society, Salt Lake City, UT. Also in 2017, the Unitarian Universalist Association's General Assembly voted to create inclusive wordings for non-binary, genderqueer, gender fluid, agender, intersex, two-spirit and polygender people, replacing the words "men and women" with the word "people." Of the six sources of the living tradition, the second source of faith, as documented in the bylaws of the denomination, now includes “Words and deeds of prophetic people which challenge us to confront powers and structures of evil with justice, compassion, and the transforming power of love.”
The Roman Catholic Church's catechism, or teaching, has no comprehensive or specific doctrine on transgender people. However, the church does traditionally equate the anatomy given at birth with gender, stating that going though processes to medically change one's body is self mutilation and sinful, "dishonoring" God's creation of that body. The church says that gender dysphoria and same sex attraction are a consequence of original sin, and that it is sinful if individuals act upon these things. Pope Francis has said "biological sex and the socio-cultural role of sex (gender) can be distinguished but not separated", furthering the belief that the sex an individual was born with is their assigned gender.
In Islamic literature, the word mukhannathun is used to describe "effeminate men". The term has sometimes been equated to transgender women, gay men, members of a third gender, or intersex individuals, though it does not neatly fit into any of those categories.
The treatment of mukhannathun varied throughout early Islamic history, and the meaning of the term took on new dimensions over time. In some eras, men deemed mukhannathun were persecuted and castrated, while in others they were celebrated as musicians and entertainers. In later years, the term came to be associated with the receptive partner in gay sexual practices, as homosexuality was seen as an extension of effeminacy. In the late medieval era, several Islamic scholars held that mukhannathun who had innate feminine mannerisms were not blameworthy as long as they did not violate religious laws concerning sexual morality.
Due to Ayatollah Khomeini issuing a fatwa allowing sex reassignment surgery for intersex and transgender individuals, Iran carries out more sex change operations than any other nation in the world except for Thailand. It is sanctioned as a supposed "cure" for homosexuality, which is punishable by death under Iranian law. The government even provides up to half the cost for those needing financial assistance and a sex change is recognised on the birth certificate.
There is a multitude of Jewish views on the issue.
The term saris, (סָרִיס) generally translated to English as "eunuch" or "chamberlain", appears 45 times in the TaNaKh. It frequently refers to a trusted but gender-variant person who was delegated authority by a powerful person. It is unclear whether most were in fact castrated. In Isaiah 56 God promises eunuchs who keep the Sabbath and hold fast to his covenant that he will build an especially good monument in heaven for them, to make up for their childlessness.
Tumtum (טומטום in Hebrew, meaning "hidden") is a term that appears in Jewish Rabbinic literature and usually refers to a person whose sex is unknown, because their genitalia are covered or "hidden". A tumtum is not defined as a separate gender, but rather a state of doubt.
Androgynos (אנדרוגינוס in Hebrew, translation "intersex") refers to someone who possesses both male and female sexual characteristics. The nature of the individual's gender is ambiguous.
Orthodox Judaism asserts that sex/gender is an innate and eternal category based on verses in the Book of Genesis about Adam and Eve and the creation of maleness and femaleness. Sex-change operations involving the removal of genital organs are forbidden on the basis of the prohibition against “anything which is mauled, crushed, torn or cut” (Lev. 22:24). A further prohibition in Deut. 22:5, proscribes not only cross-dressing but any action uniquely identified with the opposite sex, and this would also apply to an operation to transform sexual characteristics. There are, nevertheless, Orthodox authorities who recognize the efficacy of sex reassignment surgery (SRS) in changing halachic sex designation. In 2007 Joy Ladin became the first openly transgender professor at an Orthodox institution (Stern College for Women in Manhattan).
Hasidic Judaism currently makes no place for trans people, as everything in the community is determined by gender roles. Most Hasidic Jews are barely aware of trans people, and the topic is never discussed altogether. The first person to come out as trans in a Hasidic community was trans activist and writer Abby Stein, who is also a direct descendant of Hasidic Judaism's founder the Baal Shem Tov. When Stein came out she was shunned by her family, and received much scorn from the Hasidic community.
Conservative Judaism has mixed views on transgender people. In 2003 the Committee on Jewish Law and Standards approved a rabbinic ruling that concluded that sex reassignment surgery (SRS) is permissible as a treatment of gender dysphoria, and that a transgender person's sex status under Jewish law is changed by SRS. There have not yet been any openly transgender rabbis or rabbinical students affiliated with Conservative Judaism. But the Jewish Theological Seminary, one of three Conservative movement schools, openly admits students of all sexual orientations and gender identities for rabbinical training and ordination. Also,
Emily Aviva Kapor, who had been ordained privately by a "Conservadox" rabbi in 2005, came out in 2012, thus becoming the first openly transgender female rabbi in all of Judaism. In 2016 the Rabbinical Assembly, which is the international association of Conservative rabbis, passed a "Resolution Affirming the Rights of Transgender and Gender Non-Conforming People".
Reform Judaism has expressed positive views on transgender people. Reform Judaism's Central Conference of American Rabbis first addressed the issue of transgender Jews in 1978, when they deemed it permissible for a person who has undergone sex reassignment surgery (SRS) to be married according to Jewish tradition. In 1990, the Central Conference of American Rabbis declared that people who have undergone sex reassignment surgery (SRS) may convert to Judaism. In 2002 at the Reform seminary Hebrew Union College-Jewish Institute of Religion in New York, Rabbi Margaret Wenig organized the first school-wide seminar at any rabbinical school which addressed the psychological, legal, and religious issues affecting people who are transsexual or intersex. In 2003 Reuben Zellman became the first openly transgender person accepted to Hebrew Union College-Jewish Institute of Religion; he was ordained there in 2010. Also in 2003, the Union for Reform Judaism retroactively applied its pro-rights policy on gays and lesbians to the transgender and bisexual communities, issuing a resolution titled, "Support for the Inclusion and Acceptance of the Transgender and Bisexual Communities."  Also in 2003, Women of Reform Judaism issued a statement describing their support for human and civil rights and the struggles of the transgender and bisexual communities, and saying, "Women of Reform Judaism accordingly: Calls for civil rights protections from all forms of discrimination against bisexual and transgender individuals; Urges that such legislation allows transgender individuals to be seen under the law as the gender by which they identify; and
Calls upon sisterhoods to hold informative programs about the transgender and bisexual communities."  In 2006 Elliot Kukla, who had come out as transgender six months before his ordination, became the first openly transgender person to be ordained by the Hebrew Union College-Jewish Institute of Religion. In 2007 the Union for Reform Judaism issued a new edition of Kulanu, their resource manual for gay, lesbian, bisexual and transgender inclusion, which for the first time included a blessing sanctifying the sex-change process. It was written by Elliot Kukla at the request of a friend of his who was transgender. Also in 2007, David Saperstein of the Religious Action Center called for a trans-inclusive Employment Non-Discrimination Act. In 2015 the Union for Reform Judaism passed a "Resolution on the Rights of Transgender and Gender Non-Conforming People" with 9 points calling for securing and defending the rights of transgender and gender non-confirming people to respectful and equitable treatment and affirming its own commitment to continued pursuit of same.
Reconstructionist Judaism has expressed positive views on transgender people. In 2003 the Reform rabbi Margaret Wenig organized the first school-wide seminar at the Reconstructionist Rabbinical College which addressed the psychological, legal and religious issues affecting people who are transsexual or intersex. In 2013 the Reconstructionist Rabbinical Association issued a resolution stating in part, "Therefore be it resolved that the RRA [Reconstructionist Rabbinical Association] directs its executive director and board to move forward, in cooperation with the RRC [Reconstructionist Rabbinical College] and all relevant associated entities, in educating RRA members about issues of gender identity, to urge the Reconstructionist movement to similarly educate its constituency and to adopt policies that will do all that is possible to provide full employment opportunities for transgender and gender nonconforming rabbis, and to explore how the Reconstructionist movement can best influence the wider Jewish and non-Jewish world to [be] welcoming and inclusive of all people, regardless of gender identity."  In 2017, the Reconstructionist Rabbinical Association approved a resolution committing themselves to work for "full inclusion, acceptance, appreciation, celebration and welcome of people of all gender identities in Jewish life and in society at large"; the resolution also "strongly advocates for the full equality of transgender, non-binary, and gender non-conforming people and for equal protections for people of all gender identities under the law, at all levels of government, in North America and Israel."
In 1998, after she won the Eurovision song competition, a serious religious debate was held as to whether, and how, Dana International (a transgender woman) should pray in a synagogue. One rabbinical authority concluded that Dana should be counted in a minyan as a man, but could not sing in front of the community since she was also a woman, according to the rabbi, and that would violate the Orthodox rule of kol isha.
In January 2015 a transgender Jewish woman, Kay Long, was denied access to the Western Wall, first by the women's section and then by the men's section. Long's presence was prevented by "modesty police" at women’s section who are not associated with the rabbi of the Western Wall or the site administration. They are a group of female volunteers who guard the entrance to the women’s section preventing entry to visitors who are not dressed to their idea of Orthodox modesty standards for women. The director of Jerusalem’s Open House, a community center for the lesbian, gay, bisexual and transgender community, noted that Long’s experience was not unique. "Gender separation at the Western Wall is harmful for transgender people. This is not the first story that we know of with transgender religious people that wanted to go to the Western Wall and pray and couldn’t," said Elinor Sidi, who expected that the battle for access to the Western Wall for the LGBTQ community would be a long and difficult one. It was later asserted that Kay Long would have been permitted in the women's section except for her clothing. "It was not an issue of her gender, but the way she was dressed."
Several non-denominational Jewish groups provide resources for transgender people. Hillel: The Foundation for Jewish Campus Life published an LGBTQ Resource Guide in 2007. Jewish Mosaic has published interpretations of Jewish texts that affirm transgender identities. Keshet, an LGBT Jewish advocacy group, has assisted American Jewish day schools with properly accommodating transgender students.