The ecclesiastical reform movements that sharply distinguished clergy from laity also developed a means of sustaining that distinction through intensified ecclesiastical discipline. Clergy were not only freed from most forms of subordination to laypersons but also were granted legal privileges, being triable only in church courts and subject only to penalties deemed suitable by church authorities (benefit of clergy). Laity who injured clerical personnel or property were punished more harshly. But the distinction between clergy and laity also enhanced lay status. Lay authorities could legally perform judicial actions that were forbidden to clergy, like the shedding of blood or other forms of physical punishment. Clerical thinkers greatly legitimated lay activities that earlier monastic Christianity had once scorned, attributing a positive value to commerce, the law, just warfare, marriage, and other roles once considered signs of fallen and weak human nature.

The intensity of the reform movements led to a new and elaborated idea of sin and to categories of sin so grave that they required the harshest punishments, sometimes in cooperation with lay courts. The idea of crime itself, drawing on both older Roman law and earlier ecclesiastical discipline, gradually came to assume a distinctive place in secular law, as more and more conflicts that had once been settled privately came within the purview of lay legal officials. Clerical crime became a major focus of disciplinary concern. The term heresy, loosely used until the 11th century, slowly became better defined and was initially applied to clerical misconduct such as simony (the acceptance of ecclesiastical office from laymen) and nicolaitism (clerical marriage). The increasingly precise exposition of Christian doctrine by 12th-century theologians seemed to many people a displacement of the Christianity that they had always understood and practiced. Legal collections began to treat various forms of doctrinal and devotional dissent as heresy, thus formulating a category that would criminalize a wide variety of beliefs and conduct.

Promoters of the new ecclesiastical doctrine and discipline believed that the increasingly numerous devotional collectives and their charismatic leaders would eventually threaten the order of both clerical and lay society. In the early 13th century the English theologian Robert Grosseteste formulated a definition that accurately reflected the changed understanding of religious dissent: “Heresy is an opinion chosen by human faculties, contrary to sacred scripture, openly taught, and pertinaciously defended.” Criminal heresy involved belief that contradicted orthodox doctrine and was arrived at by purely human capacities. It was also belief that was publicly, and therefore seditiously, proclaimed, even after legitimate instruction by authorized teachers, thereby making the “heretic” contumacious in the eyes of the law.

Like the problem of criminal clergy, the problem of heresy raised procedural questions in law. Legal procedure in criminal cases might be initiated by an accusation by a responsible individual or by a denunciation by a group of specially appointed synodal witnesses. In 1199 Innocent III added a third procedure, that of inquisition, or inquiry by an appropriate authority, which was first used to investigate clerical crimes. Later popes appointed judges delegate as individual inquisitors, although there was not an institutionalized office of inquisition until the royal-papal establishment of the Spanish Inquisition in 1478.