Jessenius came to Prague. He was granted an audience with king Rudolf II. He managed to make the first public autopsy in the town. A body for the autopsy had got from hesitating executioner Mydlář. Jessenius became resident in Prague, and thereafter his wife came also to Prague.

Jessenius had been dismissed by the new king Matthias. He spent next winter with woman Flora. After her death, he took care of their common daughter. He became rector of the Carolinian University. After Prague defenestration and outbreak of the Bohemian revolt, he had been appointed as a delegate of revolting side and got into Hungary.