English attempts to govern Ireland had long been marked by the passing of various acts to secure its rule: in 1367, the Statutes of Kilkenny sought to prevent the Old English from any further adoption of Gaelic culture, and Poynings Law of 1494 made the Irish parliament subservient to the English one. These were approved of by the Holy See. But the English Reformation in 1533-38 under Henry VIII brought a new religious division to the relationship between Ireland and England, though he also persecuted Protestants from 1539 to 1547. In 1541 he legislated for the new Kingdom of Ireland. His son Edward VI (reigned 1547-53) was fully Protestant but his policy was only published just before his death. Queen Mary then reimposed orthodox Catholicism in 1553-58, while settling the new 'King's' and Queen's' counties in the midlands. During her reign it was agreed under the Treaty of Augsburg in 1555 that Europeans should follow their rulers' faiths (in Latin, 'Cuius regio, eius religio'). She married the future King Philip II of Spain.
Initially, English monarchs were cautious about applying the Penal Laws to Ireland because they needed the support of the Roman Catholic upper classes to put down the Gaelic Irish rebellion in the Nine Years War (1594-1603). In addition, a significant section of the Roman Catholic aristocracy was Old English who had traditionally been loyal to English rule in Ireland. However, the ascent of James I to the English and Irish thrones in 1603 and eventual victory in the Nine Years War saw a series of laws put into force. In 1605 the 'Gunpowder Plot' was planned by a tiny group of English Catholics, as they considered James I to be a heretic also, and this provided a further justification for laws restricting all Catholics in Ireland, Scotland and England. In 1607 the Flight of the Earls seeking Catholic help in Europe for a revolt led to the wholesale Plantation of Ulster.
From 1607, Catholics were barred from holding public office or serving in the army. This meant that the Irish Privy Council and the Lords Justice - who, along with the Lord Deputy of Ireland constituted the government of the country, would in future be Protestants. In 1613, the constituencies of the Irish House of Commons were altered to give Protestant settlers a majority. In addition, Roman Catholics had to pay 'recusant fines' for non-attendance at Protestant services. Roman Catholic churches were transferred to the Protestant Church of Ireland. Roman Catholic services, however, were generally tacitly tolerated as long as they were conducted in private. Roman Catholic priests were also tolerated, but bishops (who, since Catholic education was not permitter were usually trained in mainland Europe) were forced to operate clandestinely. In 1634 the issue of the "Graces" arose; generous taxation for Charles I (whose Queen Henrietta Maria was Catholic) was voted by Irish Catholic landlords on the understanding the laws would be reformed, but once the tax was voted Charles' viceroy refused two of the 51 Graces, and subsequent bills were blocked by the Catholic majority in the Irish House of Lords.
Catholic resentment was a factor in starting the Irish Rebellion of 1641 and the establishment of Confederate Ireland from 1642 with Papal support, that was eventually put down in the Cromwellian conquest of Ireland in 1649-53. After the Act of Settlement in 1652, Catholics were barred from membership in the Irish Parliament, the richer of them had most of their lands confiscated under the Adventurers Act, and were banned from living in towns for a short period. To the Cromwellians, all Catholics were, in turn, heretics. Catholic clergy were expelled from the country and were liable to instant execution when found. Many faithful had to practice their faith in secret at gathering places (such as Mass rocks) in the countryside. Seventeen Catholic martyrs from this period were beatified in 1992.
With the defeat of Catholic attempts to regain power and lands in Ireland, what became known later as the "Protestant Ascendancy" sought to insure dominance with the passing of a number of laws to restrict the religious, political and economic activities of Catholics and Dissenters. Harsher laws were introduced for political reasons during the long War of the Spanish Succession that ended in 1714. The son of James II, the "Old Pretender", was recognised by the Holy See as the legitimate king of Britain and Ireland until his death in 1766, and Catholics were obliged to support him. He also approved the appointments of all the Irish Catholic hierarchy, who were drawn from his most fervent supporters. These aspects provided the political excuses for the new laws passed for several decades after 1695. Among the discriminations now faced by Catholics and Dissenters under the Penal Laws were:
- Exclusion of Catholics from most public offices (since 1607), Presbyterians were also barred from public office from 1707.
- Ban on intermarriage with Protestants; repealed 1778
- Presbyterian marriages were not legally recognised by the state
- Catholics barred from holding firearms or serving in the armed forces (rescinded by Militia Act of 1793)
- Bar from membership in either the Parliament of Ireland or the Parliament of Great Britain from 1652; rescinded 1662-1691; renewed 1691-1829.
- Disenfranchising Act 1728, exclusion from voting until 1793;
- Exclusion from the legal professions and the judiciary; repealed (respectively) 1793 and 1829.
- Education Act 1695 - ban on foreign education; repealed 1782.
- Bar to Catholics entering Trinity College Dublin; repealed 1793.
- On a death by a Catholic, his legatee could benefit by conversion to the Church of Ireland;
- Popery Act - Catholic inheritances of land were to be equally subdivided between all an owner's sons with the exception that if the eldest son and heir converted to Protestantism that he would become the one and only tenant of estate and portions for other children not to exceed one third of the estate. This "Gavelkind" system had previously been abolished by 1600.
- Ban on converting from Protestantism to Roman Catholicism on pain of Praemunire: forfeiting all property estates and legacy to the monarch of the time and remaining in prison at the monarch's pleasure. In addition, forfeiting the monarch's protection. No injury however atrocious could have any action brought against it or any reparation for such.
- Ban on Catholics buying land under a lease of more than 31 years; repealed 1778.
- Ban on custody of orphans being granted to Catholics on pain of 500 pounds that was to be donated to the Blue Coat hospital in Dublin.
- Ban on Catholics inheriting Protestant land
- Prohibition on Catholics owning a horse valued at over £5 (in order to keep horses suitable for military activity out of the majority's hands)
- Roman Catholic lay priests had to register to preach under the Registration Act 1704, but seminary priests and Bishops were not able to do so until 1778
- When allowed, new Catholic churches were to be built from wood, not stone, and away from main roads.
- 'No person of the popish religion shall publicly or in private houses teach school, or instruct youth in learning within this realm' upon pain of twenty pounds fine and three months in prison for every such offence. Repealed in 1782.
- Any and all rewards not paid by the crown for alerting authorities of offences to be levied upon the Catholic populace within parish and county.
Historians disagree on how rigorously these laws were enforced. The consensus is that enforcement depended on the attitudes of local magistrates bringing or hearing particular cases; some of whom were rigorous, others more liberal.