The first acts of Ferdinand on the recapture of Prague were marked by an unexpected moderation. Comparatively few of the conspirators were put to death; the great bulk of them were let off with fines, or the surrender of lands; and most of the liberties of Bohemia were confirmed. But it was felt, nevertheless, that all who had sympathised with the insurrection were in a difficult and dangerous situation; and the Utraquists, who had begun the movement, combined with the Catholics, who had in many cases yielded to it, to lay the whole guilt upon the Bohemian Brotherhood.
The Bunzlau district had no doubt been conspicuous in its refusal to send forces to the Saxon war. Three or four of the lords, who were condemned for their share in the insurrection, had been known for their protection of the Brothers; and some of the Elders of the Brotherhood had ordered a day for prayer and fasting during the insurrection. It was resolved, therefore, to seize this opportunity for crushing this unpopular sect, and the chief suspicion was directed against John Augusta. He had indeed protested against the insurrection from the first, but it was proved that he had come to Prague while it was still going on; a visit to Liegnitz in Silesia was also looked upon as suspicious; while undoubtedly the chief charges against him were his known influence in the Brotherhood and his connection with Wittenberg. Even the lords who had hitherto been favourable now disowned the accused; and the Captain of Moravia, himself a member of the Society, told Augusta that he ought to have prevented the insurrection.
The Archduke Ferdinand was ordered to take measures for carrying out the intended persecution; and in the following year a Commission was appointed, which reconstituted the Town Councils in various districts, and ordered the new Councillors to proceed rigorously against the Brothers. The chief persecution began at Litomys̆l, where several men were arrested for singing hymns at the funeral of a Brother. On their refusal to abandon the Brotherhood they were imprisoned in the White Tower of the Castle of Prague; and, when threats and entreaties were found to be of no avail, they were taken from the tower and thrust into a hole into which the filth from the castle discharged itself. After some months of this treatment several of them gave way; but the others remained firm, and were at last set free on condition of withdrawing into Prussia.