In 1640 Laud published the canons framed by Convocation for the government of the English Church. With the object of clearing himself of the charge of Papistry he ordered a new persecution to be begun， but the king intervened to prevent the execution of this measure. At a time when Charles was receiving large sums of money by way of compensation for non-attendance at the Protestant services， and when he foresaw that in the conflict that was to come he could rely on the Catholic noblemen to stand loyally by him， he had no wish to exasperate the Catholics in England， or to outrage Catholic feeling in France and at Rome. In 1640， however， Parliament returned to the charge. The presence of papal agents in England， the payment of ā10，000 by the Catholic noblemen to help the king in his expedition against the Scots， and the enrolment of a Catholic army in Ireland by Strafford， were urged as arguments to prove that the king's failure to carry out the laws against Catholics was due to causes other than had been alleged. Indeed both before and after the outbreak of the Civil War (1642) the king's cause was damaged badly by his secret alliance with Rome. As a matter of fact the Catholics did rally to the standard of the king， but the persecution to which they had been subjected wherever the Parliament had control made it impossible for them to act differently. During the years that elapsed between 1642 and 1651， twenty-one victims， including priests， both secular and regular， and laymen， were put to death for their religion.[15] When at last Parliament had triumphed a new persecution was begun. An Act was passed in 1650 offering for the apprehension of priests rewards similar to those paid for securing the arrest of highway robbers.
Informers and spies were set at work， and as a result of their labours many priests were captured and confined in prison or transported. Yet， though the opponents of the king made it one of their main charges against him that he refused to shed the blood of the clergy， they adopted a similar policy when they themselves were in power. During the whole Protectorate of Cromwell only one priest was put to death in England. But recourse was had to other methods for the extirpation of the Catholic religion， imprisonment， transportation， and above all heavy fines exacted off those Catholics who held property in the country.
From Charles II. (1660-1685) Catholics had some reason to expect an amelioration of their sad condition. They had fought loyally for his father and had suffered for their loyalty even more than the Protestant loyalists. In the hour of defeat they had shielded the life of the young prince， and had aided him in escaping from enemies who would have dealt with him as they had dealt with the king. Mindful of their services and of promises Charles had made in exile， and well aware that he had inherited from his mother， Queen Henrietta， a strong leaning towards the Catholic Church， they hoped to profit by the Declaration of Breda， which promised liberty of conscience to all his subjects. But Charles， though secretly in favour of the Catholics on account of their loyalty to his father and to himself， was not a man to endanger his throne for the sake of past services， more especially as his trusted minister， the Earl of Clarendon， was determined to suppress Dissenters no matter what creed they might profess. A number of Catholics， lay and cleric， met at Arundel House to prepare a petition to the House of Lords (1661) for the relaxation of the Penal Laws. The petition was received favourably， and as there was nobody in the House of Lords willing to defend the infliction of the death penalty on account of religion， it was thought that the laws whereby it was considered treason to be a priest or to shelter a priest might be abolished. But dissensions soon arose， even in the Catholic committee itself. The kind of oath of allegiance that might be taken， the extension of the proposed relaxations so as to include the Jesuits， and the anxiety of the laymen to get rid of the fines levied on rich recusants rather than of the penalties meted out to the clergy， led to the dissolution of the committee， and to the abandonment of their suggested measures of redress.[16]
Clarendon was determined to crush the Nonconformist party notwithstanding the promises that had been held out to them in the Declaration of Breda. He secured the enactment of a number of laws， the Act of Uniformity (1662)， the Conventicle Act (1664) and the Five Mile Act (1665) known as the Clarendon Code， which， though directed principally against the Dissenters， helped to increase the hardships of the Catholic body. Once， indeed， in 1662-63， Charles made a feeble attempt to redeem his promise to both Catholics and Nonconformists by announcing his intention of applying to Parliament to allow him to exercise the dispensing power in regard to the Act of Uniformity and other such laws， but the opposition was so strong that the proposed declaration of indulgence was abandoned. The terrible fire that broke out in London (September 1666) and which raged for five days， destroying during that time a great part of the city， led to a new outburst of anti-Catholic feeling. Without the slightest evidence the fire was attributed to the Papists， and an inscription to this effect placed upon the monument erected to commemorate the conflagration remained unchanged until 1830. When Parliament met a committee was appointed to inquire into the increase of popery， and a demand was made that proclamations should be issued for the banishment of all priests and Jesuits.