The earliest Christians suffered horribly under the wicked Emperor of Rome, Nero. He was one of the first to persecute the Christians. Nero blamed the burning of Rome in 64 AD on the Christians. He then used the Christians as human torches to light his own garden. The Roman historian Tacitus wrote in his book 'Annals': "In their very deaths they were made the subjects of sport: for they were covered with the hides of wild beasts, and worried to death by dogs, or nailed to crosses, or set fire to, and when the day waned, burned to serve for the evening lights. Nero offered his own garden players for the spectacle..." The Roman persecution of Christians continued under a succession of emperors until 324 AD when Constantine the Great became emperor of Rome. Under Constantine, Christianity officially became a tolerated religion. 
Constantine was a friend to the Christians (at first); he professed to be a Christian, but he also embraced many of the pagan traditions and practices of Rome (the verdict is still out as to whether Constantine was a true born again Christian). Dave Hunt of the Berean Call says that Constantine was "the first ecumenist." Those Christians who refused to submit to the authority of the Holy Roman Empire under Constantine, their heretical doctrines and pagan practices were viewed as insurrectionists and they themselves were labeled as heretics. In 331 AD, Constantine issued an edict which ordered that any Christians not submitting to the authority of Rome be arrested, their churches and materials destroyed. Many Christians were persecuted as a result.
In John MacArthur's message The Pope and the Papacy he states, "In the long war on the truth, the most formidable, relentless and deceptive enemy has been Roman Catholicism. It is an apostate, corrupt, heretical, false Christianity, it is affront for the kingdom of Satan. The true church of the Lord Jesus Christ has always understood this. And even through the Dark Ages from 400 to 1500, prior to the Reformation, genuine Christian believers set themselves apart from that system, and were brutally punished and executed for their rejection of that system."
During the 600 year period from 1200 to 1800 A.D. known as "The Inquisition", tens of millions*of people are estimated to have been tortured and murdered for refusing to bow the knee to the "Holy" Roman Empire and/or follow her doctrines. Most of the victims of this horrible atrocity were Bible-believing Christians, but it also included "Jews and even some Roman Catholics like Joan of Arc, Savanarola, Giordano Bruno and Galileo etc."  (Also see the article "THE WALDENSES & THE ALBIGENSES‚ Defending the Pilgrim Church")
John MacArthur states,"They [the Roman Catholic Church] make laws to which they hold people. They adjudicate as to whether people have violated those laws and they mete out punishment. And through the years that punishment has been everything from excommunication to execution." (The Scandal of the Catholic Priesthood). Thankfully, the Roman Catholic Church no longer considers Protestants to be heretics, but "separated brethren". However, it's only a public relations stunt in an attempt to bring born-again Christians back "home to Rome" (maybe you've seen the billboards).
Christians are most certainly still being persecuted today by Muslims in places like the Middle East and Africa and under Communist regimes in countries like North Korea and China. In Ray Comfort's book "God Has A Wonderful Plan For Your Life" he writes, "According to Gordon-Conwell Theological Seminary, worldwide an average of 171,000 Christians annually are martyred for their faith." Yet this atrocity goes virtually unmentioned in the mainstream media. And though we have not experienced this level of persecution in the West, do not think for a moment that as Christians in America we are immuned to persecution. It is fast approaching and soon we will see who the true followers of Christ really are! (Check out The Voice of the Martyrs and Open Doors websites.)
A Lamp In The Dark: The Untold History of the Bible - Adullam Films (DVD)
FOX'S BOOK OF MARTYRS
Most people have some knowledge of the holocaust. The 6 years of torture and atrocities that the Jews suffered under Hitler and the Nazis during the Second World War. While in no way downplaying the terrible events of the holocaust, such a massacre does not compare to the severity to the torture and murder that took place under Papal authority during the 605 years of the Inquisition. From the beginning of the Papacy, until the present time, it is estimated by credible historians that more than 50,000,000, men and women have been slaughtered for the crime of heresy charged against them by Papal Rome. This Video contains actual photographs of some of the instruments of torture that were used. Since we consider this Video on the Inquisition one of the more important message that we have given, please make it known to others, and if possible post the link on your own website.
The Trial of Pope Benedict XVI - Pope Benedict confesses the sins of the Catholic church
THE POPE'S APOLOGY - Noise of Thunder Radio
PAPAL APOLOGIES - Noise of Thunder Radio
(VIDEO) DID THE CHURCH OF ROME MURDER OVER 50 MILLION CHRISTIANS FOR PREACHING THE GOSPEL AND TRANSLATING THE BIBLE INTO ENGLISH?
ESTIMATES OF THE NUMBER KILLED BY THE PAPACY IN THE MIDDLE AGES AND LATER by Prof. David A. Plaisted Ph.D
From the CBC "Historian John Cornwell has become a lightning rod for controversy with the publication of Hitler's Pope: The Secret History of Pius XII in 1999. Soon after its publication, Cornwell appears on Hot Type to explain the hullabaloo over Hitler's Pope and assess the spotty record of the 20th century's most controversial pontiff. In his autobiography entitled Seminary Boy, John Cornwell recalls running with young thugs in London's East End. But he later became a devout altar boy and studied to enter the priesthood. The Vatican gave Cornwell access to secret documents so he could disprove rumors of Pius XII's collusion with the Nazis, but instead, these papers only confirmed evidence of such claims. Despite damning allegations made against him, Pope Pius XII was declared "venerable" - a posthumous recognition of virtue - in September 2000, putting him one step closer to official sainthood. He must next be declared "beatified" (blessed), a title bestowed only on martyrs or those who have performed miracles."
Catholic Timeline of Events Relating to Jews, Anti-Judaism, Antisemitism, and the Holocaust
Hitler's Death Camps: Holocaust . . . or Inquisition?
U.S. Let War Criminal Escape to Save Vatican Face
THE VATICAN'S HOLOCAUST: The sensational account of the most horrifying religious massacre of the 20th century By Avro Manhattan