Lutheran Reformer, pioneer in church historical studies, and theological controversialist who created a lasting rift within Lutheranism.

From 1539, after studies in Venice with the humanist Baptista Egnatius, Flacius attended the universities of Basel, Tübingen, and Wittenberg. He was welcomed at Wittenberg in 1541 by Philipp Melanchthon (Melanchthon, Philipp) and there came under Martin Luther's influence. Appointed professor of Hebrew at Wittenberg in 1544, Flacius incurred Melanchthon's wrath for opposing the Augsburg Interim (1548) and the Leipzig Interim (1548), which formulated basic Lutheran beliefs. In 1549 he moved to Magdeburg, where his dispute with Melanchthon was resolved.

From 1552 Flacius was occupied with the Ecclesiastica historia, his major work in church history. Completed in 1574 and called the Centuriae Magdeburgenses (“Magdeburg Centuries”) from its third edition (1757), it treats the centuries of church history mechanically as discrete units. Under his supervision it was prepared from manuscripts collected from all accessible European libraries by a group known as the centuriators. Frequently polemical, its intent was to refute Roman Catholic claims to authenticity.

Made professor of the New Testament at the University of Jena in 1557, Flacius was soon involved in a new controversy with Melanchthon over adiaphorism, which holds that certain religious doctrines or practices are matters of indifference because they are neither commanded nor forbidden in the Bible. Melanchthon took the more liberal position that some features of Reformation theology were comparatively minor and therefore open to compromise, but Flacius maintained a strict view of Luther's beliefs and refused to yield to negotiation on any point. Following a series of personal attacks on Melanchthon, Flacius was removed from his post at Jena in 1561 and lived successively in Regensburg, Antwerp, Frankfurt, Strassburg, and again in Frankfurt.

Among other works by Flacius are Clavis scripturae sacrae (1566; “Key to Sacred Scripture”); his version (1555) of Luther's writings; and the “Book of Confutation” (1559), in which he detailed his position in the adiaphorist controversy.