The Roman Inquisition was reconstituted in 1542 to combat the menace of Protestantism in the Italian peninsula, where as the Spanish Inquisition had been created more than half a century earlier to deal with massive numbers of converted Jews. The nature of what was considered “heresy” in each system reflects these original concerns. In northern and central Italy, “Lutheranism “overwhelmingly dominated the first generation of inquisitorial activity, lasting until the 1580s. The venetian records offer a truly remarkable example: over its first 35 years (1547-1582) this holy office tried more than 700 “Lutherans” among its first 1,200 cases- plus 36 Anabaptists, 68 cases of “heresy in general,” 20 of eating meat during Lent, and almost 90 concerned with possession or reading of prohibited books. Approximately 80 percent of these early cases, therefore, concern protestant or crypto-protestant behavior. In the Venetian Terrafirma, Aquileia-Concordia showed a similar concentration on such offenses during its first 38 years (1557-1595); of its initial 380 cases, 200 or four suspected product to Paris sees and 74 for consuming meat during Lent (A possible indication of northern influences at work). In this rural area of low literacy there were only 12 cases of prohibited books. Again, over 75 percent of these cases may have involved Protestant sympathies. […]
In the Spanish portions of southern Italy our statistics suggest a different meaning in the holy office’s concern with heretics. Although a sizable share of the earliest preserved cases from Naples maybe classified as heresy trials, if you deal with protestants; in fact, through 1620 accused Mohammedans outnumbered reputed protestants by more than five to one. The diligent Spanish inquisitors uncovered large numbers of Protestants, but here too these were numerically swamped by the followers of Islam. Before 1560, the Sicilian Holy office tried more than 50 Protestants (more than any other tribunal in the Spanish system) and only eleven Moslems; but between 1560 and 1615, they judged nearly four Moslems for every protestant (471 and 138 respectively).
John Tedeschi, The Prosecution of Heresy (1991)