The issues covered by the trials and inquisitions which Foxe narrates in these books are limited and endlessly repetitive. Christology is hardly ever discussed. The taking of oaths and obedience to secular authority are raised in some cases, usually when the inquisitors are trying to pin charges of anabaptism on their victims. In the unusual case of Cranmer considerable use is made of 'lawful authority', because of his own high profile insistence upon obedience to the Royal Supremacy. Foxe is always at pains to ensure that his martyrs insist upon the lawfulness of oaths. Obedience is more difficult, and the normal response is 'we must obey God rather than man'. However this is always qualified by some statement to the effect that a Christian who is required by his conscience to disobey a lawful command will submit willingly to the penalties prescribed. Foxe is extremely sensitive to the catholic charge that protestantism is a religion of disobedience.

The issues which dominate the great majority of trials are: vernacular liturgy and scripture, and the nature and number of the sacraments. Vernacular scripture was a sensitive subject, because neither the Queen nor Pole was opposed to translation in principle, and Henry's Great Bible was never withdrawn. There were plenty of conservative clergy who thought that it should have been, and this emerges clearly from time to time, but no one is ever condemned for using an English bible. The English liturgy is a different matter, both because it was held to be specifically heretical and because its use had been banned by statute from December 1553. Challenged about their absence from approved worship, many protestants alleged their unwillingness to attend a liturgy which they could not understand, claiming that such a use was contrary to scriptural teaching, particularly that of St Paul. Foxe was also anxious to demonstrate the Edwardian orthodoxy of his martyrs, and frequently represents them as being accused of using the 1552 Prayer Book. However, the overwhelming majority of the condemnations relate to the nature and use of the sacraments. Following Luther, all protestants admitted only two, baptism and the eucharist, so anyone who denied the other five was making an heretical assertion. That, however, was seldom sufficient for the inquisitors. They did not trouble much with baptism, and the suspects were always insistent upon their acceptance of it in an orthodox sense, whatever reservations they may have had about the ritual. The eucharist was another matter entirely.

Transubstantiation was the touchstone of Catholic orthodoxy. The metaphysics of the controversy are baffling to the modern mind, and depended upon philosophical distinctions as to the nature of matter which only the most sophisticated of contemporary intellects could grasp. In the crude terms in which the debate was normally conducted, the catholic position was that the words of consecration spoken by the priest effectually converted the substances of bread and wine into the substances of the body and blood of Christ, who thereby became 'really, actually and carnally' present in the elements to the exclusion of all other substances. In spite of being invisible to the normal senses (which perceive only accidents, not substances) this body was deemed to be the same as that in which Christ had suffered death upon the cross. The consequences of this were momentous. The consecrated host itself became an object of intense veneration. Through his ability to perform this miracle of transformation, the priest became a unique vehicle of Divine authority. Through the offering of the host upon the altar at the climax of the mass, the sacrifice of Calvary was repeated.

To a protestant this whole structure of belief was blasphemous and idolatrous nonsense. The physical body of Christ had been taken up into heaven at the Ascension, and could not therefore be present on earth. Being a true natural body, it obeyed the laws of nature, and could not be present in more than one place at a time. The Lord's Supper, as they called the eucharist, was principally a commemoration of Christ's sacrifice, and secondly a demonstration of the brotherhood of the faithful. Christ might be spiritually present, to those who received in faith. This was referred to as a 'real', as opposed to a 'carnal' presence, and was a matter of dispute; but all protestants were agreed that the words of consecration were simply a reverent form of prayer. There could be no repetition of Christ's sacrifice, which had by definition been a unique event, and certainly no 'miracle'. The priest consequently derived no particular prestige or authority from administering the Supper, and the elements remained common bread and wine. They might be 'spiritually enhanced' at the moment of worthy reception, but not all reformers accepted that.

Beyond the denial of transubstantiation, and rejection of the idea that the sacrifice of Calvary could be repeated, there was no common protestant position. The precise nature of Christ's presence, if it was accepted at all, was a matter of fierce debate. Luther believed in a real presence which is best defined by his own image of fire entering into iron. This presence was 'real', and was induced by the faith, rather than the words, of the celebrant. All who received the elements absorbed it, the worthy to their benefit, and the unworthy to their damnation. No other protestant leader followed him down that road, and there was little explicit Lutheranism in England. To Hulderich Zwingli the sacrament was a sign or symbol of man's reconciliation with God, embraced by the congregation in the act of celebration. God's presence was thus ubiquitous and not confined to the elements, so Christ could not be deemed in any sense to be 'in' the bread and wine. This doctrine has been rather unfairly dubbed 'the real absence'. The most influential continental theologians in England were Peter Martyr and Martin Bucer, who agreed with Zwingli that the eucharist was a symbol of reconciliation, but were prepared to accept a spiritual presence, although they did not agree with each other over its exact nature. There was a presence specific to the elements, induced by faith rather than words, but they differed over the extent to which this presence conveyed grace to the faithful.

Cranmer's position, expressed in the Prayer Books, in the Forty Two Articles, and in numerous other writings, was influenced by both, but probably rather more by Martyr. He expressed it liturgically in the prayer of consecration, in which the celebrant petitions that the elements may 'be unto us' the body and blood of Christ. This form of presence was seen as 'real', but in a purely spiritual sense, and was effectual only for those who received in faith. To the orthodox Edwardian protestant the ungodly received only bread and wine, and the sacrament was meaningless. Although they generated a good deal of heat at the time, many of these protestant distinctions were so subtle that only the theologically sensitive could detect them at all. In this context it is important to notice that Foxe was extremely careful to make his martyrs enunciate the views of Cranmer.

Catholics regarded protestant attacks upon the mass, and particularly studied disrespect towards the consecrated host, with a horror which could easily turn into homicidal frenzy. Protestants regarded the whole rite as being at best a confidence trick designed to keep the laity in superstitious awe of the priesthood. At worst it was an example of that profane idolatry which had so often caused the God of the Old Testament to turn his back upon Israel. There could be no worse sin than to worship created matter as though it were God, and that sin was uniquely expressed in the mass. To the protestant the core of the rite was participation in the symbolic meal, which signified to the participants that they were not only united with Christ, but with each other in a true church. To the catholic reception was peripheral, except on rare occasions (normally at Easter), when extreme reverence and elaborate preparation was enjoined. It was normal for the priest to receive alone, thus expressing both his unique status and his representative function. The focus of participation then was the sacring, when the host was elevated for adoration, after the consecration. Whereas the Lord's Supper was essentially a communal act by the congregation, the mass was a private contact between the priest and God. Except at Easter the laity were present mainly to be edified by the spectacle. There was nothing new about the eucharist as a subject of controversy. Medieval heretics, particularly the Lollards, had frequently been questioned about it. The intensity of the Marian concern was a reflection of the status which the issue had achieved in the European reformation conflicts of the previous twenty years. This was partly because of its significance for the potestas ordinis, and partly because it presented opportunities for catholics to exploit protestant divisions. It was also made more incisive in England by the fact that Foxe's martyrs were in the Reformed, as distinct from the Lutheran, camp.

The 'sacrament of the altar' was thus the core of most examinations, and the most expressive of the deep theological rift which divided the parties. The other sacrament which was sometimes discussed was that of penance. The catholic believed that because of his unique intercessory status, the priest also enjoyed a special authority to forgive the sins of the penitent. It was therefore necessary to confess those sins to a priest in a spirit of remorse before absolution could be granted. Absolution thus sought and obtained became a sacramental act, that is a channel for God's grace to the faithful. Because protestants rejected the idea that a priest enjoyed any particular Divine authority, they also rejected him as a dispenser of Divine forgiveness. Penance ceased to be a sacrament, and the special function of the priest disappeared. Instead the penitent was encouraged to approach God direct in prayer, and General Confessions were included in the congregational liturgies. Refusal to attend 'auricular confession' was thus a common reason why heretics were detected or denounced. Intercession also featured in another way. Just as protestants rejected the intercessory role of the priest, so they also rejected appeal to the saints. For reasons which were probably more anthropological than theological, the church had constructed a hierarchy of intercession, modelled upon that which surrounded an earthly prince. Christ in this context was normally seen as distinct from the Father, because of that humanity which also gave him a unique intercessory function. However, the prime intecessor in the ordinary sense was the Virgin. What man did not listen to his spouse or mother? Not only did she have a woman's susceptibilities, she was especially approachable, and she, like any woman, listened to her friends, who were the saints. There was an army of the latter, each with his or her special attributes and skills. These were, or had been, real people who had struggled with real sinfulness and overcome it, making them at once sympathetic and comprehensible. This 'user friendly' structure, the protestants utterly rejected. Neither priest nor saint nor Virgin should stand between the Christian believer and his God. Moreover intercession in the catholic sense detracted from the unique honour and function of Christ.

A similar difference also affected that special type of intercession aimed at departed souls. The church had long since taken the pragmatic view that most souls were neither good enough for heaven nor bad enough for hell; and had created a place of purgation, where sins could be expiated before eventual admission into the kingdom of heaven. Unfortunately this essentially humane vision had acquired accretions, one of which was the idea that the prayers of the living could shorten the stay of the departed in purgatory, and this quickly acquired a commercial dimension. Protestants, concentrating first on the abuses, and realising that the whole structure was without scriptural foundation, rejected purgatory completely and denounced the whole idea of intercessory prayer for the dead. This struck a tender spot in the popular religious consciousness, because it greatly reduced that sense of communion between the living and the dead which had been one of the characteristics of medieval catholicism. Partly for that reason, denunciations of purgatory, or of the popular pieties of commemoration, was another common reason for heretics to be accused.

A further tactic which the inquisitors commonly used was to invite the suspect to define the church. The normal protestant response was that the church is the congregation of the faithful, in the sense understood in the Book of Acts. No catholic rejected that, but his own definition was both simpler and more tangible. The church is that body which professes allegiance to the Pope, and obeys the canon law. Since most protestants regarded the Pope as Antichrist, they were bound to reject such a statement, and thus ipso facto excommunicated themselves. Both parties accepted that there was no salvation outside the church, but whereas one was defined by a spontaneous confession of faith (and might be a matter of opinion), the other was defined by obedience to a clearly defined, and visible, authority.

Like most protestants, Foxe was deeply disgusted by the mass, and could not believe that any honest Christian could accept its doctrinal basis. Also, like the bishops he was denouncing, he regarded it as central to the quarrel between the two sides. So although matters like auricular confession, vernacular liturgies, purgatory and the definition of the church recur frequently, the argument nearly always comes back to the 'sacrament of the altar', and that priority is well attested in the formal records which he used. This was not a question of the protestants shifting the debate onto their own chosen ground. No subject aroused more passion on both sides, or demonstrated more clearly the futility of rational debate. There was simply no common ground between those who could believe in a physical body which was both ubiquitous and invisible, and those who could not.