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In the early years of Elizabeth's reign the government from motives of prudence abstained from adopting violent measures to promote the change of religion. But after 1570 there was a decided change, and particularly after 1580 the persecution was carried on with great bitterness. Many of the clergy, both secular and regular, were put to death. Amongst the latter the few Jesuits who had come into the country to help to carry on the work begun by Father David Wolf, the Franciscans, and the Dominicans, were pursued with relentless severity. Sometimes they were put to death by the soldiers without any form of trial, sometimes they were executed according to the proclamations of martial law, and sometimes they were allowed a form of trial. But the fact that they were priests was sufficient to secure their conviction. Several laymen were put to death for refusing to change their religion, for harbouring priests, or for having studied in some of the Catholic colleges on the Continent. Although Henry VIII. had succeeded in destroying many of the religious houses, still in a great part of the North, West, and South of Ireland the law had not been enforced, and even in the districts where the English held sway several of the monasteries enjoyed a precarious existence, partly owing to the kindness of certain noblemen, partly also to royal exemptions. But with the gradual subjugation of the country during the reign of Elizabeth more determined measures were taken for the suppression of such institutions. According to a return presented to the authorities in London (1578) "thirty-four abbeys and religious houses with very good lands belonging to them, never surveyed before 1569," were seized, as were also "seventy-two abbeys and priories concealed from her Majesty."[83] From a revenue return presented in 1593 it can be seen that the suppression of these houses and the seizure of their property helped considerably to strengthen the royal exchequer. From the possessions in Ireland that belonged formerly to religious houses in England the queen received annually in round numbers ￡538, from the lands belonging to St. John of Jerusalem ￡776, from those of the monastery of Thomastown ￡551, from the possessions of St. Mary's Abbey, Dublin, ￡329, and from the monasteries and other religious houses in Ireland ￡4,716.[84] The destruction of the monasteries did not, however, mean the extinction of the Mendicant Orders. They still continued to maintain themselves in the country, so that during the worst days of the seventeenth century the Franciscans and Dominicans were to be reckoned with as the most dangerous opponents of the religious policy of the English government.

Only in case of one bishop, the notorious Miler Magrath, was Elizabeth able to secure submission. He was a Franciscan friar, who, having been sent to Rome to petition that the vacant See of Down and Connor should be conferred on Shane O'Neill's brother, took steps to secure the appointment for himself (1565). Finding on his return that he could not hope to get any revenue from his diocese on account of the opposition of O'Neill, he made his submission to the queen (1567) and received as his reward the diocese of Clogher, and later on the Archbishopric of Cashel (1570). For the greater part of his term of office as archbishop he held the Sees of Waterford and Lismore, and when he resigned them in 1607 he obtained a grant of Achonry and Killala. While pretending to be scandalised by the toleration shown to Catholics, and especially to Catholic officials, and to be anxious that the laws should be enforced with the utmost rigour he took measures to warn the clergy whenever there was danger of arrest. On one occasion when he was in London, having learned that a raid was contemplated against the priests, he wrote to his wife to warn Bishop MacCragh of Cork to go into hiding at once, and to send away the priests who had taken refuge in his own palace at Cashel lest he should get into trouble. He was denounced by the officials in Dublin as a traitor, a drunkard, and a despoiler of the goods of the Church. He sold or leased the property of his dioceses, kept a large number of benefices in his own hands solely for the sake of the revenue, appointed his own sons, his daughter, and his daughter-in-law to parishes to provide them with an income, built no schools, and allowed the churches to go into ruins. His children made no secret of the fact that they were Catholics, and the archbishop himself seemed to think that though Protestantism had been useful to him in life, the old religion would be preferable at death. In 1608 faculties had been granted to Archbishop Kearney of Cashel for absolving Magrath from the guilt of heresy and schism. Some years later he besought a Franciscan friar to procure his reconciliation with Rome, promising that for his part, if the Pope required it, he would make a public renunciation of Protestantism. This request of his was recommended warmly to the Holy See by Mgr. Bentivoglio, inter-nuncio at Brussels, but the love of the archbishop for the revenues of Cashel and of his other bishoprics and benefices seems to have proved stronger than his desire for pardon, for he continued to enrich himself and his friends at the expense of the State Church till his death in 1622. It was believed by his contemporaries that on his death-bed he abjured his errors, and was reconciled with the Church by one of his former religious brethren.[85]

The destruction of the religious houses and collegiate churches during the reigns of Henry VIII., Edward VI., and Elizabeth dealt a heavy blow to Irish education. Here and there through the country, clergy and laymen contrived to teach schools and to give their pupils a sound knowledge of the classics as well as of the language, literature, and history of their country. But the theological colleges were closed; Oxford and Cambridge were no longer safe training-places for Irish ecclesiastics, and unless something could be done at once there was grave danger that when the bishops and clergy, who were then at work, passed away, they would leave none behind them to take their places. Fortunately the close and direct communication between Ireland and the Catholic nations of the Continent suggested a possible method of preventing such a calamity, by the establishment, namely, of Irish colleges in Rome, France, Spain, and the Netherlands. These institutions owed their existence to the efforts of Irish bishops and priests, and to the generous assistance of the Popes, and the sovereigns of Spain and France. They were supported by the donations of individual benefactors, by grants from the papal treasury or the royal treasuries of Spain and France, and by the fees paid by students, some of whom were wealthy enough to bear their own expenses, while others of them were ordained priests before they left Ireland so that they might be able to maintain themselves from their /honoraria/ for Masses.

In Spain Irish colleges were established at Salamanca, Seville, Alcalá, Santiago de Compostella, and Madrid. The college at Salamanca was founded by Father Thomas White, S.J., a native of Clonmel, with the approval of Philip II., in 1592 under the title of /El Real Colegio de Nobles Irlandeses/. The King of Spain provided a generous endowment, and the control of the college was entrusted to the Jesuits. Shortly after its foundation complaints were made in the names of O'Neill and O'Donnell that the administrators of the college showed but scanty attention to the claims of students from Ulster and Connaught (1602), a complaint which seems to be justified by the rolls of matriculation, on which the names of very few students from these provinces are to be found. Those who presented themselves at Salamanca took an oath to return to labour in the Irish mission after the completion of their studies, and to enable them to do this a certain sum of money was granted to them from the royal treasury of Spain to cover the expenses of the journey to Ireland. Many of the most distinguished of the Irish bishops and priests during the seventeenth century were men who had graduated at Salamanca.[86] The college at Compostella was founded in 1605, was endowed partly by Philip III., and was placed in charge of the Jesuits. It served as an auxiliary to Salamanca, and its students were sent there for their theological training. The College of the Immaculate Conception at Seville owed its origin (1612) to some of the Irish secular clergy. It was endowed very generously by Philip III. who placed the Jesuits in control of it in 1619. To help to provide for the support of the students the Irish merchants, who carried on a brisk trade with Seville and Cadiz at this period, bound themselves to bestow on the college a certain percentage on every cask of wine they shipped, while Paul V. granted permission to the fishermen of the province of Andalusia to fish on six Sundays or holidays on condition that they devoted the results of their labours to the support of the Irish College. The college at Madrid was founded by Father Theobold Stapleton (1629), and was used principally as a hospice for the reception of Irish priests who had completed their studies, and who came to the Spanish capital to receive the money guaranteed by the king to enable them to return to Ireland. In 1657 George de Paz y Silveira, who was related on his mother's side to the MacDonnells of Antrim, founded a college at Alcalá principally for students from the North of Ireland. According to the directions of the founder the election of the rector was vested in the hands of the student body, a regulation that led to grave disorders, and finally to the closing of the college. The Irish college at Lisbon owed its existence to the activity of the Jesuits, notably of Father John Holing. It was opened in 1593, but it was only two years later that owing to the kindness of a Spanish nobleman a permanent residence was acquired, over which Father White, S.J., was placed as rector. A community of Irish Dominican Fathers was opened at Lisbon, as was also a convent of Dominican Nuns.

Irish students received a friendly welcome not merely in Spain, but also in the Spanish Netherlands. From the middle of the sixteenth century several ecclesiastical students from Ireland fled to Louvain for their education, but it was only in 1623 that Archbishop MacMahon of Dublin succeeded in founding a separate institution, the celebrated /Collegium Pastorale/ for the training of secular priests for the Irish mission. Out of his own private resources he founded six burses in the college, and at his earnest request six others were endowed by the Propaganda. The college was formally approved by Urban VIII. in 1624, and Nicholas Aylmer was placed over it as its first rector. Though many of the ablest of the Irish bishops and priests of the penal times were educated in the Pastoral College, still Ireland is even more indebted to another Irish establishment at Louvain, the Irish Franciscan College of St. Anthony of Padua. At the petition of Florence Conry, Archbishop of Tuam, himself a Franciscan and a devoted supporter of the Northern Chiefs, Philip III. recommended the project of an Irish Franciscan College to his representative in the Netherlands, and conferred on the institution a generous endowment. With the blessing and approval of Paul V. the college was opened formally in 1609, and so great was its success that it soon became the leading centre of Irish missionary activity. Here Irish scholars like John Colgan, Hugh Ward, Father Mooney, Bonaventure O'Hussey, Hugh MacCaghwell, etc., found a home, and from the Louvain Irish printing- press were issued a large number of catechisms, religious treatises, and historical works, that did incalculable service for religion and for Ireland. Another very important institution at Louvain was the Irish Dominican Priory known as the Holy Cross founded in 1608. A seminary for the education of secular priests was opened at Antwerp in 1629 as a result of the exertions and generosity of Father Laurence Sedgrave and his nephew Father James Talbot. It was supported from the revenues bestowed upon it by its founders, from the grants of the papal nuncio at Brussels, and from the donations of Irishmen, laymen as well as clerics. At Tournai a seminary for Irish priests was founded by Father Christopher Cusack, and its students attended lectures in the college belonging to the Jesuits. Nearly all the Irish establishments in the Netherlands continued their work until they were destroyed during the troubled period that followed on the outbreak of the French Revolution.

In France, too, Irish students found a welcome and a home. Colleges set apart entirely for their use were opened in Paris, Douay, Lille, Bordeaux, Toulouse, and Nantes. The Irish College in Paris may be said to date from the year 1578, when Father John Lee and a few companions from Ireland took up their residence in the Collège Montaigu. Later on a friendly nobleman, John de l'Escalopier, placed a special house at their disposal, and Father Lee became the first rector of the new seminary, which was recognised officially by the University of Paris in 1624. Later on the Collège des Lombards was acquired, as was also the present house in the Rue des Irlandais. The college in Paris was favoured specially by the Irish bishops, as is evident from the fact that in the year 1795 more than one-third of the Irish clerical students on the Continent were receiving their training in the French capital. The seminary in Douay was founded by Father Ralph Cusack in 1577. At that time Douay belonged to the Spanish Netherlands, and the Irish seminary participated in the boundless generosity of the Kings of Spain. The Irish seminary at Lille was founded also by Father Cusack, and was placed under the control of the Capuchins. Though it was intended principally for the use of students from the province of Leinster, special attention was devoted to the Irish language, without a knowledge of which no person could be appointed rector. The seminary at Bordeaux was founded (1603) by Father Diarmuid MacCarthy, a priest of the diocese of Cork, and later on it received special grants and privileges from the queen-regent, Anne of Austria. The same kind benefactress provided a home for the Irish students at Toulouse (1659), while a few years later a seminary for Irish students was established at Nantes.

Very early in Elizabeth's reign the question of providing priests for the Irish mission engaged the earnest attention of the Roman authorities. Gregory XIII. had arranged for the establishment of an Irish college in Rome, and had provided the means for its support, but as an expedition was then being prepared to aid James Fitzmaurice in his struggle in Ireland, the project was postponed, and the money was devoted to the purposes of the war. In 1625 the Irish bishops addressed a petition to the Holy See praying for the establishment of an Irish college in Rome. Cardinal Ludovisi, then Cardinal Protector of Ireland, supported strongly this petition. He secured a house for the accommodation of a few students, and in 1628 the college was opened. In his will the Cardinal provided generously for the endowment of the college, and he also expressed a wish that it should be entrusted to the care of the Jesuits. They entered into control in 1635, and directed the affairs of the college till a short time before the suppression of the Society.[87]

Elizabeth and her advisers were not slow to see the danger of allowing Irish youths to be educated in Rome, France, or in the territories of the King of Spain. For years the English government had been advised to take measures for the establishment of a good system of English schools as the best means of conquering the country. It was suggested that with the suppression of the monasteries and the wholesale confiscation of their possessions something might be done by Henry VIII. or Edward VI. for the cause of education.[88] But these hopes were doomed to speedy disappointment. The revenues of the religious houses, which had provided centres of learning for the boys and girls of the country, found their way into the royal treasury or into the pockets of the dishonest commissioners, and no educational establishments were erected in their place. The Deputy did, indeed, inform the canons of St. Patrick's, Dublin, that their church should be converted to a better use, namely, a university, but the promise was made only to induce them to surrender without a struggle. The valuable church plate, crosses, etc., were melted down and handed over to the mint.[89]

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