In medieval Europe, attitudes toward homosexuality varied from region to region, determined by religious culture; the Catholic Church, which dominated the religious landscape, considered sodomy as a mortal sin and a "crime against nature". By the 11th century, "sodomy" was increasingly viewed as a serious moral crime and punishable by mutilation or death. Medieval records reflect this growing concern. The emergence of heretical groups, such as the Cathars and Waldensians, witnesses a rise in allegations of unnatural sexual conduct against such heretics as part of the war against heresy in Christendom. Accusations of sodomy and "unnatural acts" were levelled against the Order of the Knights Templar in 1307 as part of Philip IV of France's attempt to suppress the order. These allegations have been dismissed by some scholars.

Although homosexuality was not considered a major offense during the early Roman Empire, homosexual encounters and homosexual behavior came to be viewed as unacceptable as Christianity developed. The Hebrew Bible (Leviticus 18:22, 20:13, Deuteronomy 22:5) condemned females who wore male attire, males who wore female attire, and males that engaged in homosexual intercourse. In the 11th century the Benedictine monk and cardinal Peter Damian wrote the Liber Gomorrhianus, an extended attack on both homosexuality and masturbation. He portrayed homosexuality as a counter-rational force undermining morality, religion, and society itself, and in need of strong suppression lest it spread even and especially among clergy.

Hildegard of Bingen, born seven years after the death of St. Peter Damian, reported seeing visions and recorded them in Scivias (short for Scito vias Domini, "Know the Ways of the Lord"). In Book II Vision Six, she quotes God as condemning same-sex intercourse, including lesbianism; "a woman who takes up devilish ways and plays a male role in coupling with another woman is most vile in My sight, and so is she who subjects herself to such a one in this evil deed".

In the 13th century, the theologian Thomas Aquinas was influential in linking condemnations of homosexuality with the idea of natural law, arguing that "special sins are against nature, as, for instance, those that run counter to the intercourse of male and female natural to animals, and so are peculiarly qualified as unnatural vices." This view points from the natural to the Divine, because (following Aristotle) he said all people seek happiness; but according to Aquinas, happiness can only finally be attained through the beatific vision. Therefore, all sins are also against the natural law. However, the natural law of many aspects of life is knowable apart from special revelation by examining the forms and purposes of those aspects. It is in this sense that Aquinas considered homosexuality unnatural since it involves a kind of partner other than the kind to which the purpose of sexuality points. Indeed, he considered it second only to bestiality as an abuse of sexuality.

Around 400, Christianity began to introduce a new sexual code focused on the religious concepts of holiness and "purity". The emerging Church, which gained social and political sway by the mid-third century, had two approaches to sexuality. One of these, like their Greco-Roman predecessors, did not view or judge sexuality in terms of heterosexual or homosexual acts. Instead, it only judged the act itself, and promoted a sex life that mainly focused on platonic relationships. For instance, the Roman tradition of forming a legal union with another male by declaring a "brother" persisted during the early medieval years. Also, though there was no official marriage within religious communities, long-lasting relationships or bonds were made. Also, there are many poems from that century that suggest the existence of lesbian relationships.

By the end of the Middle Ages, most of the Catholic churchmen and states accepted and lived with the belief that sexual behavior was, according to natural law, reserved for procreation, considering purely sterile sexual acts (i.e., oral and anal sex, as well as masturbation) sinful. However, homosexual acts held a special place as crimes against natural law. Most civil law codes had punishments for such "unnatural acts", especially in regions that were heavily influenced by the Church's teachings.^{[citation needed]}

In the early medieval years, homosexuality was given no particular penance; it was viewed like all the other sins. For example, during the eighth century, Pope Gregory III gave penances of 160 days for unnatural female acts and usually one year for males who committed acts of sodomy, the passive partner being treated more severely. During the Inquisition itself, individuals were rarely investigated for sodomy alone; it was usually associated with the expression of heretical beliefs and attacks on the Church. Those who did not recant their heresy would be severely punished. Officials saw a break in moral and religious views because of homosexuality. Thus, it was seen as a pagan view; those considered guilty would be charged with capital punishment.

The Papal restoratio of the 11th century led to increasingly harsher attitudes towards sodomites. The Council of Nablus in 1120, in the Kingdom of Jerusalem, enacted severe penalties for sodomy in the aftermath of the defeat of the Antiochene army at the Field of Blood the year before. In the 13th century France, sodomy resulted in castration on the first offense, dismemberment on the second, and burning on the third. Lesbian behavior was punished with specific mutilations for the first two offenses and burning on the third as well. By the mid-14th century, in many cities of Italy, civil laws against sodomy were common. If a person was found to have committed sodomy, the city's government was entitled to confiscate the offender's property.