The respite granted the brethren through the intercession of Žerotin did not last long. Every year the persecution of all in Bohemia who were outside the pale of the Church of Rome became severer and their position more precarious. At a secret meeting of the brethren in 1625, at which Komenský was present, it was decided altogether to abandon Bohemia, and a discussion arose as to the country where the members of the Unity should seek refuge. It was finally decided that the brethren should separate, some proceeding to Poland, others to Hungary and Transylvania. Poland then had a large Protestant population, and this is still the case as regards the two other countries mentioned. Before finally leaving Bohemia, it was decided that messengers should be sent out in different directions to obtain information as to where the brethren could find quarters. Komenský, with two companions, started for Poland. In that country Count Raphael Lescynski, himself a member of the Unity, was known as a warm friend of the brethren.

During his journey Komenský first heard of the so called prophecies of one Christopher Kotter. Characteristically enough Komenský immediately forgot all other preoccupations and obtained an interview with the "prophet." Henceforth his belief in Kotter was implicit, and he immediately decided on translating into Latin and into Bohemian the German prophecies, which are a tissue of absurdities.[101] The fact that a generally respected Protestant divine as Komenský had desired an interview with Kotter of course greatly increased the man's celebrity. Even the Elector of Brandenburg, and Frederick, ex-king of Bohemia, requested that he should be presented to them. From Germany Komenský continued his journey to Poland, and having, as he tells us, received satisfactory assurances from Count Lescynski, he returned for the last time to Bohemia towards the end of the year 1626.

He here again fell under the influence of a visionist, in whom he thoroughly believed, and whose hallucinations he even many years afterwards considered worthy of being recorded in print. Julian Ponatovská, an impecunious Polish nobleman, had been received as a member of the Unity and appointed preacher at Mladá Boleslav. When the communities of the brethren were dispersed, Charles of Žerotin secured Ponatovská's safety by appointing him to the office of librarian at his castle at Naměst in Moravia. Christina, Ponatovská's daughter, appears to have been of a highly hysterical nature, which, added to the intense religious excitement of the times, induced her to deliver "prophecies," which were generally received with the greatest interest. The pathological side of the question need not be dealt with here. It is sufficient to state that Christina, who had recently been reading the Revelation of St. John, declared that she had heard the voice of the Lord, who had chosen her as intermediary for the purpose of informing the faithful of the approaching defeat of Rome.

It was the misfortune of Komenský to be brought accidentally into contact with the "prophetess." Christina had not joined her father in Moravia, but remained at Branna in Bohemia, not far from Třemešna, where Komenský was then staying. Christina suddenly became dangerously ill at Branna, and as the minister of the Unity who resided at Třemešna happened to be absent, Komenský was sent to Branna in his stead. He has given a rather curious account of his visit to the prophetess. She appeared to be in a state of ecstasy, and constantly repeated the words "Bridegroom, bridegroom!" Somewhat later she began to communicate her prophecies to Komenský and the other persons present. She again prophesied that the Protestants would shortly obtain a complete victory over Austria and the Pope. To these prophecies also Komenský gave immediate implicit faith. Though he soon left Branna, he remained in communication with Christina. The latter soon recovered from her illness, but continued to prophesy; her prophecies, indeed, became even more definite. She now announced that, through the will of her heavenly bridegroom, Jesus, Papacy would be abolished; that the Turks would be converted to Christianity, and that Ferdinand II. and Wallenstein would perish by violent deaths. Wallenstein was then residing at Jičin in Bohemia, and Christina, accompanied by a female friend, proceeded there to acquaint him with her prophecies. The great general was not at home, but Countess Wallenstein, who saw Christina, was greatly embarrassed, and consulted some Jesuits on the subject of her visionary visitor. The Jesuits advised that Christina should immediately be sent to jail; but it was finally agreed merely to remind her of the decree that had already banished from Bohemia all members of the Unity. Wallenstein was, on his return home, informed of the visit of the prophetess. He smiled, and remarked that the Emperor indeed received messages from Rome, Constantinople, and Madrid, but that he had received one from heaven.

Christina returned to Branna, and as her father had died meanwhile, she decided to join Komenský and his wife—he had remarried very shortly after the death of his first wife—and a party of other exiles, who were on the point of leaving Bohemia. They set out in January 1628; and on crossing the frontier of their country in the direction of Silesia, "they all knelt down and prayed to God with cries and many tears, entreating Him that He would not finally avert His mercy from their beloved country nor allow the seed of His word to perish within it." In February Komenský arrived at Lissa, a small town in that part of Poland that is now known as the Prussian province of Posen. Ponatovská for some time continued a member of Komenský's household, and the controversy concerning the true inspiration of her prophecies raged for a considerable time. A joint meeting of doctors and ministers of the Unity did not settle the question, as the opinion of the doctors was in direct opposition to that of the ecclesiastics, of whom Komenský was one. The latter never wavered in his belief in Christina's prophecies.[102] He maintained that it could nowhere be proved that the Church had been deprived of the gift of prophecy. Before dismissing Christina Ponatovská it should be stated that some time after these events she married a young man employed at the printing-work of the Unity at Lissa, had two sons and three daughters, and in later years "disliked all reference to her prophecies."

It would, however, be doing Komenský bitter wrong if we supposed that he was, while at Lissa, exclusively occupied with the prophecies of Kotter and Ponatovská.

The period of his first residence at Lissa was, on the contrary, one of incessant and fruitful hard work. His duties as a preacher and schoolmaster were fulfilled with equally great conscientiousness, and, from the few sermons that have been preserved, it appears that in this respect also his ability was exceptional. It was also at this time that most of Komenský's educational works were written, though many were re-modelled later. It is therefore very difficult to fix the chronological order of Komenský's works, and even to decide whether the Bohemian or the Latin version of some of them is the original one. The beginning of the "pansophic" studies also dates from this time, and the Physica, Komenský's first philosophical work, was completed as early as in 1632.

Of external events there is at this period of Komenský's life little that requires mention. The monotonous life of the brethren was only occasionally interrupted by the echoes of the events of the Thirty Years' War. In 1631 the news of Gustavus Adolphus's great victory at Breitenfeld, and in the following year that of the occupation of Bohemia by the Saxons, reached Lissa. I have already noticed the brief and vain hopes that Komenský founded on these events.

It is worthy of notice that even in those troublous times Komenský's literary work soon became known. His "pansophic" studies, that appeal so little to modern readers, then attracted almost more attention than his really valuable educational works. Among those who appear to have taken an early interest in Komenský's "pansophy" was Samuel Hartlib, a learned Englishman, who was probably of German origin, "who resided in London, and took a keen interest in everything that savoured of intellectual progress."[103] Hartlib seems, indeed, first to have heard of Komenský as the author of Janua Linguarum, an educational work that then, and even long after, enjoyed great celebrity; but he was principally interested in Komenský's philosophical studies. Hartlib entered into correspondence with him, requested information on the subject of "pansophy," and offered pecuniary assistance should Komenský wish to visit England.