The Reformation movements divided Christian Europe into competing and often warring denominational factions. Defining one's religious affiliation therefore became even more important a task than during the era of the medieval inquisition. In the pre-Reformation era, Catholic preachers and inquisitors had spread anxiety about heretics and blasphemers drawing down divine retribution in plagues or catastrophes, while inquisitions and judicial action proved fairly effective in suppressing most heretical movements across Europe by 1500. However, not all dissidents had given up their unorthodox beliefs; in many cases they had learned only to be very cautious in expressing them publicly, some following the example of Nicodemus, the disciple of Jesus who kept his affiliation secret.

Concealment of heterodox beliefs had also been suspected of the Lower Rhine mystics and especially of the supposed members of the ‘Brethren of the Free Spirit’, which was hardly the organized sect that inquisitors portrayed it to be. The mystical tendency to internalize spirituality was taken by the orthodox to imply depreciation, even renunciation, of external religious forms, and at times there was some truth to this suspicion. Such misgiving quickly became attached to the famed Dutch humanist Erasmus of Rotterdam (1466–1536), who satirized popular devotion to saints, relics and sacramentals. The late medieval Devotio Moderna's emphasis on the inner reception of the sacraments was seen by many churchmen as potentially anticlerical.

In 1673 the Roman Inquisition began its investigation into the unusual case of Isaac Nabrusch, who, during his several periods of exile, confessed to having crossed the boundaries that normally delineated Judaism, Islam, Greek Orthodoxy and Catholicism, puzzling his investigators with his sincerity in each of his ‘conversions’. About a century earlier, the French Calvinist minister Jean de Léry (1534–c. 1613) returned to France from exile in Brazil, then used his knowledge of the cannibalism of Brazil's Tupí people to critique the religious wars ravaging his home country. These are merely two examples, drawn from the thirteen essays in this volume, of individuals whose exile from their homeland for religious reasons allowed them, or perhaps forced them, to reconsider their individual religious identity. While doing so, some of them also began to rethink the nature of religion itself. For most, the experience of losing their home for the sake of the faith was traumatic, though they demonstrate a variety of reactions and experiences.

The experiences of these exiles were hardly marginal to the larger developments taking place in the early modern period. After all, this was an era fundamentally marked by religious conflict, intolerance and persecution. During an era in which nearly every ruler in Europe assumed that the political and social order depended on securing some degree of religious uniformity within the territory, the frustrating persistency of religious dissent posed existential challenges for all.