It was strict Holy Office practice to keep detailed records of all its proceedings from the first summons to the final sentencing. This was intended to discourage the inclination to ask leading questions which would suggest to the accused how they should reply. A permanent member of every court of inquisition was the Notary, who took down in writing every question and every answer, including the exclamations of pain emitted by the victims of torture. Each official took a solemn vow of secrecy, held interrogations in strict privacy, and carefully guarded the records of trial proceedings. There were several reasons for this. First, witnesses had to be protected from possible retaliation by the family and friends of the accused. Second, once a defendant named his accomplices, the Holy Office might have to move swiftly to bring them into custody. If word leaked out to them before they could be apprehended, the system would not be very effective. Third, the reputation of the accused had to be protected. It was often reiterated that inquisitors should act cautiously when making an arrest.

An inquisitor of Genoa wrote:
If, after the presentation of evidence through the prosecution witnesses, and the completion of the interrogation of the accused, the suspect had not cleared himself nor confessed to the charges, he was allowed to prepare his defense. The suspect received a notarized copy of the entire trial conducted up to that point, with the charges against him in the vernacular, so that he might more easily understand them. He was allowed a previously determined period of time to study the evidence against him, and to prepare a series of questions intended to counter the testimony of his accusers He could also call friendly witnesses to testify in his behalf.
If the accused failed to take advantage of his right to legal defense, the testimony was considered accepted by him, and he threw himself on the mercy of the court. But by no means was the possibility for a defense to be denied when the suspect requested it, even if a confession had been obtained. Despite such provisions, it would have been difficult for anyone unpracticed in the law to create and present an effective defense. The inquisition recognized this. When the accused declared that he lacked experience in such matters and required the services of a lawyer, his wishes were granted. The suspect was allowed to suggest the names of three lawyers, one of whom was assigned by the court to serve him. Legal aid was not reserved for the wealthy. If the accused did not have sufficient funds to pay legal fees, the court paid the lawyer. However, the lawyer-client relationship was a curious one when compared to today's practice. If a lawyer became convinced that his client was indeed guilty and that the client would not be persuaded to abandon his error, the attorney was obliged to discontinue the defense. Lawyers who continued to defend the "obviously guilty" often were subsequently held as suspects themselves. If the lawyer was not convinced of his client's guilt, then he could aid in the suspect's defense by presenting extenuating circumstances (i.e., drunkenness, anger, insanity, etc.). He could also seek postponements, delays in court proceedings, while attempting to shift the focus of the court to other witnesses who may have perjured themselves with inconsistent testimonies. Lawyers often prepared apologies for their clients and argued against interrogations involving torture. Attorneys losing cases would also plea for mild sentences for their clients. A defendant could know the evidence against him, but not necessarily the names of his accusers. At the beginning of his defense proceedings, the accused was required to name any people who he suspected to be testifying against him out of malice. If he was right, the inquisitor was obliged to investigate the motives and credibilities of those witnesses. After examination of such testimonies, if it was found that the depositions were false, these witnesses could be held for perjury. All of this was not taken lightly by the inquisitors. Records show that many of the "guilty" had previously presented false witness.
Interrogation with torture usually was prescribed in two general situations. First, where the evidence clearly indicated guilt which the suspect had denied or was incapable of disproving, and second, when it was deemed that a confession had not been full and sincere, or when it was felt that all of the accomplices had not been named. Those who were spared from torture were pregnant women, or women who had given birth within a forty day period, the elderly, children under fourteen and the physically impaired. Torture was rigidly controlled and restrictions were enforced in Roman practice. The judge could not proceed to interrogation under torture unless the evidence was compelling and the defense had presented its case. Nor did the inquisitor alone decide whether torture was justified. He had to seek the opinion of an advisory council consisting of theologians and lawyers. If torture was to be used, the court had to follow the instructions for torture, issued by the Supreme Tribunal of Rome. Deviations from accepted procedure were not tolerated by Rome (however, many variations of torture did occur under the provincial tribunals). A curious side note: When the defendant sustained torture without changing his testimony or confessing, the evidence, in many cases was considered purged and absolution was given. As one might guess, the inquisitors attempted to protect themselves from this eventuality by recommending a careful scrutiny of all the particulars in the case, the nature of the evidence, the quality of witnesses, and the duration of torture and the force with which it had been administered. When and if a confessional was obtained, sentences were ordinarily reviewed in Rome before they were pronounced. Convicted offenders, both lay and clerical, might be sentenced to monastic confinement. This confinement was generally of two types: First was the more formal confinement in a cell. The second permitted circulation about the grounds of monastery or convent with the suspect relegated to solitary penance. House arrest, or the restriction of movement to a geographical area ranged from the size of one's own house to his village or even a city (i. e., Rome). The elderly, or those with large families were usually sentenced to house arrest. Fulfillment of the terms of house arrest was assured by adequate monetary security (bonds). More severe penalties took the form of galley sentences, and the most severe was capital punishment. A death sentence handed down by the inquisition meant burning at the stake. However, only a small percentage of cases concluded with capital punishment. The most frequently prescribed sentences were public humiliation in the form of abjuration and salutary punishment which was prescribed for three types of offenders: 1) the obstinate and unrepentant; 2) those offenders who "relapse", and 3) those who had been convicted of attempting to overturn the cardinal doctrines of the Church (i.e., the Virgin birth, the full divinity of Christ).
The final act in the inquisitional process was the auto da fe, a public ceremony where, after sentencing, penitent heretics abjured and were reconciled to the church, and the obstinate and relapsed offenders were sent to their fate. An interesting closing note: Many of the people sentenced to burning at the stake were first hanged or beheaded. The few who were burned alive at the stake were offered sacks of gunpowder, which, when placed around their heads, resulted in a quicker death.

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