Persecutions against the Catholic Church took place during the papacy of Pope Pius XII (1939–1958). Pius' reign coincided with World War II (1939–1945), followed by the commencement of the Cold War and the accelerating European decolonisation. During his papacy, the Catholic Church faced persecution under Fascist and Communist governments.

The Nazi persecution of the church was at its most extreme in Occupied Poland. The defeat of Fascism at the end of World War II ended one set of persecutions, but strengthened the position of Communism throughout the world, intensifying a further set of persecutions – notably in Eastern Europe, the USSR, and, later, the People's Republic of China. The Catholic Church was under attack in all Communist governed countries and lost most of its existence in Albania, Bulgaria, Yugoslavia, Romania, Communist China and the Soviet Union (including Estonia, Latvia and Lithuania).

Fascist persecutions The Catholic Church was repressed by Nazi Germany starting after the signing by the Vatican of a concordat (Reichskonkordat) with Nazi Germany in 1933, hoping to protect the rights of Catholics under the Nazi government. The terms of the concordat were violated by the Nazis. The Nazi persecutions were also adopted to various degrees by Nazi allies and puppet regimes during World War II (1939–1945). The Catholic Church in Germany was systematically repressed by the Nazis and persecution was at its most severe in Nazi occupied Poland, where churches, seminaries, monasteries and convents were systematically closed and thousands of priests and nuns were either murdered, imprisoned or deported.

According to John Cornwell, the Church was faced with a dilemma: compromise with the governments in order to maintain a structure with which to survive, or resist or confront and risk annihilation.Cornwell 333 To save its faithful, the Vatican attempted both at varying times.

Nazi persecutions

Germany The Catholic Church had been a leading opponent of the rise of the National Socialist German Workers Party through the 1920s and early 1930s. Upon taking power in 1933, and despite the Concordat it signed with the church promising the contrary, the Nazi Government of Adolf Hitler began suppressing the Catholic Church as part of an overall policy of to eliminate competing sources of authority. The Nazis arrested thousands of members of the German Catholic Centre Party as well as Catholic clergymen and closed Catholic schools and institutions. As the Third Reich expanded, thousands more Catholic priests were imprisoned or killed and Catholic institutions disbanded by the Nazis.

According to Hitler's biographer Alan Bullock, Hitler was a "man who believed neither in God nor in conscience ('a Jewish invention, a blemish like circumcision')".Alan Bullock; Hitler, a Study in Tyranny; HarperPerennial Edition 1991; p216 Bullock wrote: Hitler thought that Catholic teachings, taken to their conclusion, "would mean the systematic cultivation of the human failure".Alan Bullock; Hitler, a Study in Tyranny; HarperPerennial Edition 1991; p218 Bullock adds that "once the war was over, [Hitler] promised himself, he would root out and destroy the influence of the Christian churches, but until then he would be circumspect":Alan Bullock; Hitler, a Study in Tyranny; HarperPerennial Edition 1991; p219

Alfred Rosenberg was the original draftsman and spokesman of the Nazi Party program and official ideologist of the Nazi Party. He was a rabid anti-Semite and anti-Catholic. In his "Myth of the Twentieth Century", published in 1930, Rosenberg proposed to replace traditional Christianity with the neo-pagan "myth of the blood":

Rosenberg and Hitler's senior lieutenant Martin Bormann actively collaborated in the Nazi program to eliminate Church influence – a program which included the abolition of religious services in schools; the confiscation of religious property; circulating anti-religious material to soldiers; and the closing of theological faculties.

The Nazi Government closed down Catholic publications, dissolved the Catholic Youth League and charged thousands of priests, nuns and lay leaders on trumped up charges. The Gestapo violated the sanctity of the confessional to obtain information. Erich Klausener, the President of Catholic Action in Germany, delivered a speech to the Catholic Congress in June 1934, criticizing the government. He was shot dead in his office on the Night of the Long Knives of 30 June. His entire staff was sent to concentration camps. Church kindergartens were closed, crucifixes were removed from schools, the Catholic press was closed down and Catholic welfare programs were restricted on the basis they assisted the "racially unfit".

Many German clergy were sent to the concentration camps for voicing opposition to the Nazi authorities, or in some regions simply because of their faith. Many Catholic laypeople also paid for their opposition with their lives. Over 300 monasteries and other institutions were expropriated by the SS.

The Vatican issued two encyclicals opposing the policies of Mussolini and Hitler: Non abbiamo bisogno in 1931 and Mit brennender Sorge in 1937, respectively. The Catholic Church officially condemned the Nazi theory of racism in Germany in 1937 with the encyclical "Mit brennender Sorge", signed by Pope Pius XI. Smuggled into Germany to avoid prior censorship and read from the pulpits of all German Catholic churches, it condemned Nazi ideologyFrattini, p. 230 as "insane and arrogant". It denounced the Nazi myth of "blood and soil", decried neopaganism of Nazism, its war of annihilation against the Church, and described the Führer as a "mad prophet possessed of repulsive arrogance". It was written partially in response to the Nuremberg Laws and as response to the persecution of the church.

Following the outbreak of World War II, the Vatican under Pope Pius XII pursued a policy of neutrality. The Holy See advocated for peace and spoke against racism, selfish nationalism, atrocities in Poland, the bombardment of civilians, and other issues.Encyclopædia Britannica's Reflections on the Holocaust: Pius XII – World War II and the Holocaust The Pope allowed national hierarchies to assess and respond to their local situations, but established the Vatican Information Service to provide aid to thousands of war refugees, and saved further thousands of lives by instructing the church to provide discreet aid to Jews.

Poland

According to Norman Davies, the Nazi terror was "much fiercer and more protracted in Poland than anywhere in Europe." Nazi ideology viewed ethnic "Poles" – the mainly Catholic ethnic majority of Poland – as "sub-humans". Following their 1939 invasion of West Poland, the Nazis instigated a policy of genocide against Poland's Jewish minority and of murdering or suppressing the ethnic Polish elites, including religious leaders. In 1940, Hitler proclaimed: "Poles may have only one master – a German. Two masters cannot exist side by side, and this is why all members of the Polish intelligentsia must be killed."United States Holocaust Memorial Museum: Poles: Victims of the Nazi Era

The Catholic Church was brutally suppressed in Poland. Between 1939 and 1945, an estimated 3,000 members (18%) of the Polish clergy were killed; of these, 1,992 died in concentration camps.Craughwell, Thomas J., The Gentile Holocaust Catholic Culture, Accessed July 18, 2008 During the 1939 invasion, special death squads of SS and police arrested or executed those considered capable of resisting the occupation, including professionals, clergymen and government officials. The following summer, the A-B Aktion (Extraordinary Pacification Operation) by the SS rounded up several thousand Polish intelligentsia and saw many priests shot in the General Government sector.

Historically, the church had been a leading force in Polish nationalism against foreign domination; thus the Nazis targeted clergy, monks and nuns in their terror campaigns. Treatment was at its most severe in the annexed regions, where churches were systematically closed and the majority of priests were either murdered, imprisoned or deported. Seminaries and convents were closed.

Eighty per cent of the Catholic clergy and five bishops of Warthegau were sent to concentration camps in 1939, where 1,992 Polish clergy died throughout the period; 108 from Warthegua are regarded as blessed martyrs. Around 1.5 million Poles were transported to work as forced labor in Germany. Treated as racially inferior, they had to wear purple P's sewn into their clothing – sexual relations with Poles was punishable by death. In addition to the genocide of the Polish Jews, it is estimated that 1.8 to 1.9 million Polish civilians were killed during the German Occupation and the war.

Elsewhere During the Nazi occupation of the Netherlands, the Dutch Bishops condemned the Nazi abduction of Jews. The Nazis retaliated with a series of repressive measures. Many Catholics were involved in strikes and protests against the treatment of Jews, and the Nazis offered to exempt converts and Jews married to non-Jews if protests ceased. The Archbishop of Utrecht and other Catholics refused to comply, and the Nazis commenced a round up of all ethnically Jewish Catholics. Some 40,000 Jews were hidden by the Dutch church and 49 priests killed in the process. Among the Catholics of the Netherlands abducted in this way was Saint Edith Stein, who was murdered at Auschwitz.

Japanese persecutions

The expansion of Imperial Japan across the Asia Pacific from 1941 was accompanied by many atrocities against Catholic missionaries, clerics, nuns, and lay people. Imperial Japan had developed State Shinto as the Imperial religion and promoted the notion of the divinity of the Emperor. Japanese propaganda identified Catholics with European dominance – especially among Japan's own small Catholic community but also larger Asian communities in East Timor, Korea, French Indo-China the Dutch East Indies, the Philippines, Singapore, Hong Kong, Australian Papua, Australian New Guinea and elsewhere.

In the majority Catholic Philippines, priests and seminarians were interned. The five Columban priests killed at Malate are remembered as the Malate Martyrs.

In Australian New Guinea, priests and religious were imprisoned in concentration camps. From 1943, Japanese toleration of Christianity had shifted to confrontation.Peter To Rot; Australian Dictionary of Biography; online 17 July 2014 Troops interfered with Catholic religious practices and destroyed church buildings. Some 100 Catholics were killed for continuing to catechise. The martyr Peter To Rot took up duties as a catechist after Japanese invaders imprisoned the local missionaries. Forms of worship were forbidden following the Battle of the Coral Sea and To Rot was arrested and executed by the Japanese in 1945. He became the first Melanesian to be beatified in 1995.

Communist persecutions The Catholic Church was repressed following the World War II, during the Cold War, by the Soviet Union and the Communist states in Eastern and Central Europe.

In East Germany and Hungary, the Church was subjected to ongoing attacks, but was able to continue some of its activities, however on a much reduced scale. In Albania, Bulgaria, Czechoslovakia and Hungary, persecution continued to the point that the Church faced extinction. In the Soviet Union and mainland China, the Catholic Church largely ceased to exist, at least publicly, during the pontificate of Pope Pius XII.

Church diplomacy