With the decline of the Roman Empire, and its replacement by various barbarian kingdoms, a general tolerance (with the sole exception of Visigothic Spain) of homosexual acts prevailed. As one prominent scholar puts it, "European secular law contained few measures against homosexuality until the middle of the thirteenth century." (Greenberg, 1988, 260) Even while some Christian theologians continued to denounce nonprocreative sexuality, including same-sex acts, a genre of homophilic literature, especially among the clergy, developed in the eleventh and twelfth centuries (Boswell, 1980, chapters 8 and 9).

The latter part of the twelfth through the fourteenth centuries, however, saw a sharp rise in intolerance towards homosexual sex, alongside persecution of Jews, Muslims, heretics, and others. While the causes of this are somewhat unclear, it is likely that increased class conflict alongside the Gregorian reform movement in the Catholic Church were two important factors. The Church itself started to appeal to a conception of "nature" as the standard of morality, and drew it in such a way so as to forbid homosexual sex (as well as extramarital sex, nonprocreative sex within marriage, and often masturbation). For example, the first ecumenical council to condemn homosexual sex, Lateran III of 1179, stated that "Whoever shall be found to have committed that incontinence which is against nature" shall be punished, the severity of which depended upon whether the transgressor was a cleric or layperson (quoted in Boswell, 1980, 277). This appeal to natural law (discussed below) became very influential in the Western tradition.