He was the son of the artisan and council leader Christoph Krafft and a student at the Breslau/Wroclaw Gymnasium of St. Elisabeth and Mary Magdalene.

[1][2] From 1535 onwards, Crato studied theology and lived six years in the household of Martin Luther in the University of Wittenberg.

[4] He kept a diary during his time in Wittenberg which was used as a source for Johannes Aurifaber's influential edition of Luther's Table Talk (Colloquia oder Tischreden Doctor Martini Lutheri).

[2] With the support of the Breslau city council and the recommendation of Philipp Melanchthon and Joachim Camerarius the elder, Crato studied medicine at the University of Padua from 1546.

He was a student of the famous medical professor Johannes Baptista Montanus, who exercised a decisive influence on Crato's first works.

That year he married the daughter of the city secretary Johannes Scharf von Werd and began his family.

As a representative of an irenic Melanchthonian-Calvinist orientation, Crato struggled against the Gnesio-Lutheran followers of Matthias Flacius Illyricus As a prominent representative of Humanist "school" medicine, Crato suffered a severe professional embarrassment when an unlearned female practitioner was called in to serve at the death bed of the emperor.

He secured his release in the fall of 1581, and he retired to his estate Rückers in the County of Glatz, then an integral dominion of the Bohemian crown, which he had acquired in 1567.

Crato befriended some of the leading intellectuals of his time including Camerarius, Volcher Coiter, Henri Estienne, Thomas Erastus, Konrad Gessner, Paulo Aldo Manutio II., Johannes Sambucus, Piero Vettori, and Theodor Zwinger, Georg Joachim Rheticus[4] among others.

Crato and court surgeon Peter Suma, performed the first autopsy documented in writing on October 13, 1576 in Regensburg on the deceased Emperor Maximilian II.

The internal organs of the emperor were placed in a gold-plated copper pot that was buried on the left side of the high altar in the Regensburg Cathedral.