Following the 1948 Czechoslovak coup d'état, he was arrested by the StB, the secret police of the communist regime in Czechoslovakia, and imprisoned on charges of high treason.

Following the 1989 Velvet Revolution, Gojdič was posthumously honoured by post-communist Czechoslovakian President Vaclav Havel[2][3] and beatified by Pope John Paul II in 2001.

[4] For his role in saving 1500 Jewish lives during the Holocaust in Slovakia,[5] Bishop Gojdič was posthumously honoured as a Righteous Among the Nations by Yad Vashem in 2007.

After the Slovak parliament confirmed a special law permitting the expulsion of Jews from Slovakia, Gojdič wrote a protest against the cruel deportations which were being carried out by the Collaborationist Hlinka Party.

On 26 October 1942, the Slovak Hlinka Guard informed the Ministry of the Interior that high number of fictitious conversions to Byzantine Catholicism were taking place.

According to the security service report, Bishop Gojdič had personally held a fictitious conversion ceremony to save Jewish lives in the town of Michalovce.

[10] After the end of hostilities, Slovak Jews whose lives had been saved by Bishop Gojdič foresaw that he would be in danger from the new Communist government and repeatedly offered, through the Bricha organization, to smuggle him to the West.

[10] Foreseeing the 1948 Czechoslovak coup d'état well in advance, with the help of a new auxiliary, Bishop Basil Hopko, Gojdič launched a campaign to reinforce the faith of his people by mobilizing every possible means: visits, missions, retreats, the radio, and the press.

Slovak Jewish Holocaust survivors whose lives he had saved wrote a letter in his defense to the then-Prime Minister of Czechoslovakia Antonín Zápotocký, but to no avail.

[10] In January 1951, a trial "high treason" began against three Catholic bishops (Ján Vojtaššák, Michal Buzalka [sk], and Gojdič) he was given a life sentence.

[1] At the prison of Ruzyň an official informed him that from there he could go straight to Prešov, on the sole condition that he agree to become patriarch of the Orthodox Church in Czechoslovakia.

[1] Pope John Paul II said during his homily for the occasion, "Known to the people as 'the man with a heart of gold,' he became known to the representatives of the government of the time as a real 'thorn in the side.'

Thus for him began a long calvary of suffering, mistreatment and humiliation which brought about his death on account of his fidelity to Christ and his love for the Church and the Pope.