Established religious communities in Hungary also participated in the rescue operations, although in different ways and to a different extent.

The representative of the Holy See in Budapest, Nuncio Angelo Rotta used all his authority to take a firm stand against the persecutions. In the Transdanubian region Baron Vilmos Apor, Catholic bishop of Győr became one of the main opponents of exclusion and deportations, and later of the terror implemented by the Arrow Cross. He raised his voice in opposition to the atrocities committed against the Jews. He asked for a meeting with the prime minister to discuss these issues, but Sztójay declined to receive him. The bishop prepared memoranda and called repeatedly on Archbishop Jusztinián Serédi to issue a pastoral letter. In his letter sent to the minister of interior, he condemned locking up Jews in ghettos "which contradicts all humanity and the spirit of Christianity, punishing innocent people without fair and impartial judgment."

In a letter sent to Serédi on 15 June, he hinted at the responsibilities of the higher clergy that remained silent about the rural deportations. "How shall we stand in history, if we remain in apparent agreement and maintain polite relationship with a government which tortures thousands and thousands all over the country with utmost cruelty, depriving them of all their human rights and assisting their deportation to slave labor and death" – he asked. Bishop Apor also saved Roma, rounded up for deportation. His conduct proved to be an example: during the autumn marches to Hegyeshalom, priests and population of Catholic villages along the road to Vienna provided assistance in many cases, in spite of the fact that this was prohibited.

In Szombathely, Bishop Sándor Kovács protested first from the pulpit, later to government members against the inhuman measures. The pro-German government did not accept his interventions, but using his local connections, he was still able to save several Jewish lives. For the benefit of Jews in Pécs and its region, Bishop Ferenc Virág succeeded in alleviating the circumstances during their stay in ghettos, but the brutal end, deportation to Auschwitz-Birkenau could not be avoided.

In northern Transylvania, Bishop Áron Márton condemned many times in staggering words the grave and fatal measures. On 18 May in Kolozsvár (Cluj, present-day Romania), he called for compassion and assistance to those in need. He stated that "in defense of justice and in service of love, being persecuted and imprisoned is not shameful but glorious." Because of his public condemnations of the Jewish policy of the Sztójay government, he had to leave Hungary and continued his life at the bishop's residence in Gyulafehérvár/Alba Julia, Romania.

The number of children separated from their families in the turmoil of the war increased steadily. In most cases, religious organizations and officials took care of them. Compassionate people escorted those without support to aid organizations, Red Cross shelters, and church institutions. During the siege of Budapest by the Soviets, they had to be sheltered from the bombardments and shelling.

The "Good Pastor" action by the Reformed Church played an outstanding role in rescuing mothers and children in groups. Within this program, with the support of Friedrich Born, delegate of the International Red Cross in Budapest, shelters were established for Jewish children and children of Jewish origin. Hundreds were taken care of and saved ingeniously from deportation. Gábor Sztehlo, commissioned by the Lutheran Church, organized 32 homes for children, providing refuge to 1600 children and 400 adults. Dr. Emil Koren Lutheran pastor and his wife were also part of his voluntary staff.

In the Lutheran church on Deák square in the capital, Pastor András Keken and his wife provided fearless assistance. Almost fifty Jewish lives were saved by issuing Christian birth certificates and by accommodating some of those in need. Pastor Albert Bereczky contributed to rescue operations by issuing fake certificates of baptism and providing hiding places. Father Pál Klinda placed Jewish women in a military sewing facility. With this imaginative move, he saved eighty to a hundred lives.

Benedictine Father Ferenc Köhler also demonstrated great courage. In November 1944, he assisted the Jews marching on the Vienna road to be "loaned" to Germany. Similarly to Tibor Báránszky, Köhler also used protecting letters of the Nuncio's office to rescue sick and elderly people from the crowd and transport them back to Budapest. In December, he also visited the central ghetto, providing medicine and food. The Chairman of the Adventist Church, László Michnay provided fake documentation to many people. He hid ten people, among them the poet Andor Peterdi in his own flat. In 1964, he was among the first Hungarians to receive the Righteous Among the Nations award in Jerusalem.

Gennaro Verolino and his Hungarian collaborators carried out self-sacrificing rescue operations from the Nuncio's office in Buda castle. On several occasions, Captain Géza Bakos helped them to protect church institutions. Aggregate data suggest that some fifteen thousand Jews were saved by protecting letters of the Vatican during the Arrow Cross rule.

They accommodated and managed to hide successfully the Jews that took refuge in church institutions in the capital. By doing this, they took great risk: if discovered, they could have easily shared the destiny of fellow rescuers, Mátyás Varsányi, Lutheran pastor of Buda and field chaplain Ferenc Kálló. During Easter of 1944, Kálló preached on the radio. Because of his openly antiwar statements, the transmission was interrupted, but he stuck to his views. He became the spiritual leader of rescue actions in Garrison Hospital 11. Many writers, artists, medical doctors found refuge here. Following the takeover by the far right, his life came under threat, nevertheless he continued his work. On 28 October, armed Arrow Cross members dragged him from his sickbed and executed him in the Budakeszi forest. The secretary general of the Hungarian Association of the Holy Cross, József Cavallier was gravely wounded in the official premises. The deportation of several catholic priests to Dachau also figures on the list of sins of the Arrow Cross. Gusen, one of the auxiliary camps of Mauthausen, saw the end of the life of Reformed Church Pastor Dr. Zsigmond Varga.

The Society of Social Brethren, under the leadership of Margit Schlachta accommodated a large number of Jews in their buildings in Budapest and throughout the country. In the home for working women in Bokréta street however, there was a traitor. Based on denunciation, the Arrow Cross dragged away and shot into the icy Danube Vilma Bernovits faith instructor and Sára Salkaházi social sister.

Salkaházi, Righteous Among the Nations, was beatified in the presence of tens of thousands in Budapest on 17 November 2006.

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