The various Christian denominations had faced the moral issue of anti-Jewish sentiments for many centuries before the Holocaust. Whether Catholic, Orthodox or Protestant, the Churches had to some degree fostered these sentiments, especially by spreading the false message that the Jews were collectively responsible for killing Jesus. Over the previous thousand years there had been many localised pogroms, deportations and persecutions of Jewish communities throughout Europe in which the Churches had often played a leading role.

The events that unfolded between 1933 and 1945 were, however, unique in the history of Christian-Jewish relations. The persecution of the entire German Jewish community before 1939, and then the systematic rounding up and slaughter of millions of Jews, Slavs and Gypsies confronted the Churches with an unprecedented challenge to their standing as the guardians of a moral order for good, standing above the ordinary affairs of states, politicians and diplomats.

Although many individual clergy and laity acted to uphold the moral position of the Churches, most of the leaders of Christianity failed to meet the challenge posed by Nazism. There are many reasons for this: centuries of antisemitism had led the Churches to believe that Judaism should be eliminated altogether; many Church leaders saw the major threat of the 1930s and 1940s as atheistic communism in Stalin's Russia; some Churches took advantage of the situation to recruit the followers of other faiths (e.g., the Catholic Church in Croatia and Bosnia which actively participated in forced conversions of Orthodox Serbs); and all the Churches were more concerned about their own survival than challenging Hitler's policies.

The German Churches, both Protestant and Catholic, were mainly concerned to survive under Hitler's anti-Christian rule. Some clergy did oppose euthanasia of the disabled, others defended Jewish converts to Christianity and some such as Canon Lichtenberg of Berlin and the famous theologian Dietrich Bonhoeffer played honourable roles in opposing Nazism. In the main, however, the German Churches remained silent as their Jewish neighbours were stripped of their rights, forced into exile, deported and finally annihilated. While this was going on many clergy were preaching antisemitic sermons, praying for a Nazi victory, attending to the spiritual needs of the Army and generally reinforcing the legitimacy of Hitler's policies.

Throughout Nazi-occupied areas there were similar responses by the Churches. In Holland, France, Greece, Norway and Denmark many Church leaders issued public protests against the deportation of Jews. In Hungary and Rumania Papal Nuncios briefly stopped deportations, while in Yugoslavia, Bulgaria and Greece the Orthodox Church actually rescued some Jews from deportation. The Russian Orthodox Church in the main threw their support behind the war effort while remaining silent and inactive during the mass killings.

Some Catholic Church leaders played an important part in rescuing Jews, especially in Belgium, France, Italy and Holland, while in Istanbul Monsignor Roncali (later Pope John XXIII) spared no effort in helping Jews to find safe havens. Many other Catholic leaders actively participated in the Holocaust, including the leader of the Slovak State, Josef Tiso (a priest), Bishop Šaric of Sarajevo in Bosnia and Bishop Buchko of the Ukrainian Uniate Church. Pope Pius XII did almost nothing against the numerous clergy and laity who ordered and carried out the Holocaust throughout Nazi-occupied Europe.

In the 1920s Pius XII had been a Vatican diplomat in Germany where he developed a strong pro-German position. He personally gave Hitler money to help build the tiny Nazi Party in the 1920s. As the Vatican's Secretary of State, in 1933 he made a Concordat with Hitler to preserve the position of the Catholic Church, and then invested much of the Vatican's wealth in the booming Nazi economy of the mid-1930s. Just before World War II broke out, his predecessor (Pius XI) was preparing to issue a strong denunciation of Nazism when he suddenly died. Pius XII quietly buried the denunciation and spent the next six years issuing only vague messages of sympathy for "the victims of injustice", even though the Vatican knew from 1941 what Nazi policies meant to Jewish and other victims.

Like most senior Catholic leaders, Pius XII believed that Stalin's brand of communism was the greatest threat to the Church's survival. On at least two occasions Western officials asked the Pope to make protests against the Holocaust and he refused on the grounds that if he did he would also have to criticise Stalin. After the war, the Vatican organised escape networks to help Nazis evade justice, especially those who came from countries occupied by the Russians. This was described by those involved as an "act of Christian charity," but it certainly contrasts starkly with the Church's role during the Holocaust.

Pius XII's failure to act decisively during the Holocaust can be traced to his belief that the Church's role as a state, with its own diplomats, secret service and banking system, was more important than its universal role, standing above the affairs of humanity and intervening as a moral force for good. This was later partly recognised by Pope John XXIII, who initiated a process to examine the Vatican's role during the Holocaust and wrote a Prayer for Penance shortly before his death in 1963. It is difficult, however, to escape the conclusion that Pius XII's failure was, in fact, the failure of the entire Vatican hierarchy of the time.