The New Testament is more ambiguous about gender-variant identities than the Old Testament. Eunuchs (Greek eunochos, similar to Hebrew saris) are indicated as acceptable candidates for evangelism and baptism, as demonstrated in a story about the conversion of an  Ethiopian eunuch. At one point, 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." This has sparked discussion about the significance of the selection of the Ethiopian eunuch as being the first gentile conversion to Christianity. Some argue that the inclusion of an eunuch represents a sexual minority similar to some of those who are included under today's category of transgender, in the context of the time.

Modern Christian denominations vary in their views, but some are accepting. Unitarian Universalism is a liberal religion with roots in liberal Christianity, and it was the first denomination to accept openly transgender people as full members with eligibility to become clergy, and the first to open an Office of Bisexual, Gay, Lesbian, and Transgender Concerns. 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. The United Church of Christ General Synod called for full inclusion of transgender persons in 2003. In 2005 Sarah Jones became the first openly transgender person ordained by the Church of England as a priest. Carol Stone was the first transgender priest, having been ordained in 1978 and transitioning in 2000, then continuing her ministry within the church as a woman. In 2008, the United Methodist Church Judicial Council ruled that 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 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. In 2014 Megan Rohrer became the first openly transgender leader of a  Lutheran congregation (specifically, the Grace Evangelical Lutheran Church of San Francisco.) 

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