The definitive rupture between Hus and the Roman Catholic Church, "the principal beginning of accusations and grievances against me," as Hus himself wrote, was brought on by events which had vast importance for the whole Christian world. The schism in the Western Church still continued, in spite of many efforts to effect a reconciliation between the two rival groups of cardinals and their respective leaders. France therefore decided no longer to recognise as legitimate either of the two claimants to the papal throne, Benedict XIII. and Gregory XII., and to remain neutral up to the time that a general meeting of the cardinals of both parties should have chosen a new pontiff. Bohemia was one of the countries that had hitherto recognised the "Roman Pope," Gregory XII., but King Wenceslas, no doubt honestly wishing to re-establish the unity of the Church, decided to follow the example of the King of France. He therefore brought the matter before Archbishop Zbyněk, and also consulted the university of Prague. The Archbishop immediately answered that he would never forsake the allegiance of Pope Gregory. At the university opinions differed. The Bohemian "nation", of which Hus was now the recognised leader, was strongly in favour of the king's proposition. The Bavarian and Saxon "nations", as well as the Polish one—which then consisted principally of Germans from Silesia—took the opposite view. At a general meeting held under the presidency of Henry of Baltenhagen, a German who was then rector, it was decided that the university should continue to recognise Gregory XII. as the legitimate Pope. Hus energetically defended the proposal that the university should declare to remain neutral up to the time that a new and legitimate Pope should have been chosen, and he thus incurred the particular enmity of the Archbishop. At the end of the year 1408 a decree was placarded in Bohemian and Latin on the doors of the churches of Prague, stating that Hus, "as a disobedient son of the holy mother, the Church," was forbidden to exercise any ecclesiastical functions. Hus addressed an eloquent letter to the Archbishop defending his conduct, but it made no impression on the mind of that ecclesiastic.

An important indirect result of the decision of the university was that a fundamental change in its organisation now took place. After the vote by which it had been decided to ignore the king's wishes, and to refuse to accept neutrality in the struggle between the two Popes, both parties at the university sent deputations to Kutna Hora (Kuttenberg), where Wenceslas and his court were then residing. The representatives of the Bohemian party, who were headed by Hus, no doubt hoped for a favourable reception, as they alone had maintained the views of the king with regard to the papal schism. They were, however, mistaken. The king received them very ungraciously, and even accused Hus and other Bohemian magisters of being the cause that Bohemia had acquired the evil reputation of being a heretical country. On the other hand, the king was most gracious to the German magisters, who had probably come to apologise for their opposition to the royal will, and he assured them that he would maintain all their privileges.

A complete change in the views of the ever-vacillating king took place in the following month. At that moment Nicholas of Lobkovic, a man of learning, and, it is said, a friend of Hus, had obtained considerable influence over Wenceslas. As "supreme notary", or director of the Bohemian mines, Lobkovic resided at Kutna Hora, then an important mining centre, and he was thus thrown into constant contact with the king at this time. Under his influence, Wenceslas, in January 1409, published the "Decrees of Kutna Hora", which entirely changed the constitution of the university of Prague. As has already been mentioned, the university was divided into four nations, three of which—perhaps contrary to the intentions of Charles IV., the founder of the university—always voted together, and were jointly known as the German nation. The Bohemians were thus in their own country permanently in a minority. A complete change was effected by the decrees of Kutna Hora. The king stated that, "whereas the German nation, possessing no rights of citizenship in the kingdom of Bohemia, has hitherto held three votes" (at the university), "while the Bohemian nation, the lawful heiress of that kingdom, possessed and enjoyed but one, we consider it unjust and most improper that foreigners should enjoy in abundance the profits" (i.e. benefices, foundations, &c.) "of the natives, who consider themselves aggrieved by this deprivation, and we declare that the Bohemian nation shall, ... according to the regulations existing in favour of the French at the university of Paris, and according to similar rules which exist in Lombardy and Italy, possess in future three votes at all councils, judgments, examinations, and other acts and dispositions of the university."[35] Four days later a decree of the king forbade all persons in Bohemia, both ecclesiastics and laymen, to continue their allegiance to Pope Gregory.

All resistance to the king's will now ceased at the university. In the year of the publication of the decrees of Kutna Hora, all German professors and students, that is to say, all those members of the university who supported Pope Gregory, and were opposed to Church reform, left Prague. The university now became a stronghold of that party which was favourable to Church reform, as well as to the national aspirations of the Bohemian people. It was but natural that the reconstituted university should choose John Hus, the leader in the struggle, as its rector, though he had already held that office a few years before.

The position of Hus was now more assured and more prominent than at any previous period. His popularity with the Bohemian people, who attributed to him the change in the regulations of the university so favourable to their nationality, was greater than ever, and they flocked to his sermons in the Bethlehem chapel in even greater numbers than before. King Wenceslas was grateful to Hus for his aid in obtaining the neutrality of the university during the schism in the Church, and his consort, Queen Sophia, made no secret of her veneration for the great preacher whose sermons at Bethlehem she often attended. Archbishop Zbyněk, indeed, continued inimical to Hus, but circumstances rendered it for the moment difficult for him to harm the preacher at Bethlehem. The Council of Pisa had deposed both claimants to the papal throne, and had elected a new pontiff, who took the name of Alexander V., and who was recognised by the greatest part of Europe. The two previously elected Popes did not renounce their claims, and still found followers. The Archbishop of Prague, who still recognised Gregory, was therefore naturally without influence on Pope Alexander. It was thus for the moment fruitless that the Archbishop appointed an "inquisitor" who was to inquire into the complaints raised against Hus and his followers, and specially into the right of Hus to continue preaching at the Bethlehem chapel. Hus entirely ignored these proceedings, and some of his followers even brought before Pope Alexander a complaint against the conduct of the Archbishop, stating that he had raised false accusations against them. The matter went so far that Zbyněk was summoned to appear before the new pontiff.

On September 2, 1409, Archbishop Zbyněk—inconsistently, as Hus maintained—renounced the allegiance of Pope Gregory, and recognised Alexander as the legitimate pontiff. The reconciliation between the generally recognised Pope and the Archbishop of Prague had a marked influence on the destiny of Hus. The united strength of the Roman Church is now directed against him, and matters proceed much more rapidly. As early as December 20, 1409, a decree of Pope Alexander stated that, "through the action of the enemy of the human race, recently in the city of Prague, the kingdom of Bohemia, the marquisate of Moravia, and other provinces, the false opinions—savouring of heresy and division of the Church—once brought forward by the condemned heresiarch, John Wycliffe, have been fully circulated, particularly with regard to the sacrament of the altar."[36] The letter continues to declare that in future no sermons shall be preached except in "cathedrals, collegiate churches, parish churches, and churches belonging to monasteries." This was directly aimed at Hus, whose Bethlehem chapel fell under none of the categories mentioned above. The letter or decree ended by instructing the Archbishop to appoint four doctors of theology and two doctors of canon law, under whose advice he was to proceed against those who spread the heretical tenets referred to. The Archbishop was to oblige all such persons to recant their erroneous opinions, and to deliver up for destruction all MSS. of the works of Wycliffe which they might possess. Should they refuse to do this the Archbishop was not only to deprive them of all benefices that might be in their hands, but he was also to invoke the aid of the "secular arm" against them.

The papal decree, for reasons that are not known, only reached Prague in March of the following year, and was made public on the 18th of that month. Hus appealed to Pope Alexander, and again somewhat later to his successor, John XXIII., but both appeals remained without result. While awaiting the papal decision, Hus had, in company with some of his adherents, delivered up about two hundred volumes containing writings of Wycliffe; they declared that if it were proved that these writings contained matter contrary to the doctrine of the Church, they were prepared publicly to recant such errors.

Archbishop Zbyněk had, meanwhile, after consulting the doctors of theology and canon law, issued a decree forbidding all preaching except in the places specified by the papal command; at the same time he ordered that all the copies of Wycliffe's works that had been made over to the ecclesiastical authorities should be immediately burnt. It is probable that the decision of the Archbishop, which he published at a meeting of the synod of the archdiocese on June 16, was known before that day. On the same day, the 16th of June, the members of the university already protested against the intended burning of Wycliffe's works. They maintained that sufficient time had not elapsed since the writings of Wycliffe had been delivered over, and that it was impossible that a thorough examination of the theological tenets contained in them should already have taken place. They also stated that many of these writings had no connection with questions of dogma, but dealt with logic, philosophy, natural history, and similar matters. However, neither Hus's appeal to the Pope nor the declaration of the university, nor the appeal to King Wenceslas, in which that learned body begged that the burning of the books be at least deferred, was of any avail. On July 16 two hundred books containing writings of Wycliffe, some—as the contemporary chronicler tells us—beautifully bound, were solemnly burnt in the courtyard of the archiepiscopal palace, in the presence of the Archbishop, the members of the chapter, and many other priests. This measure was followed two days later by the solemn sentence of excommunication pronounced by the Archbishop against Hus and his adherents.

The burning of Wycliffe's works met with almost general disapproval in Prague. A chronicler, writing probably shortly after these events, tells us: "Instantly a great sedition and discord began. Some said that many other books besides those of Wycliffe had been burnt; therefore the people began to riot; the courtiers of the king were incensed against the canons and priests; many opprobrious songs against the Archbishop were sung in the streets."[37]

The rioting in Prague became so serious, that Wenceslas, who had been absent, returned hastily to his capital, and while ordering that the owners of the books of Wycliffe that had been burnt should be compensated, he forbade, under penalty of death, the singing of opprobrious songs, which had been one of the causes of the riots. Hus and his adherents were still confident that the Pope would, in consequence of their appeal, cancel the decree of the Archbishop. In the meantime they determined to defend publicly the orthodoxy of some of Wycliffe's works which the Archbishop had condemned. In the then usual manner a meeting of the university was convoked, before which Hus, on July 28, defended the orthodoxy of Wycliffe's treatise, De increata, benedicta et venerabili Trinitate. On the following days some of his adherents, before the same forum, defended other works of Wycliffe.[38] Hus also continued, in spite of the Archbishop's prohibition, to preach at the Bethlehem chapel, and his services were more crowded than ever. When Hus read to his audience a letter he had received from Richard Wyche,[39] an English adherent of Wycliffe, and in the name of the Church of Christ in Bohemia saluted the Church of Christ in England, more than ten thousand people are stated to have been present at the sermon.