In Japanese history there were times when rulers favored the spread of Christianity, and periods when imported from overseas creed was in disgrace, and his followers had been cruel. In the XV and XVI centuries, Christianity spread rapidly in the Islands of the archipelago, but at the end of the sixteenth century was banned, and the people of Japan practiced it secretly. Residents of Nagasaki were forced every year to prove that they are not Christians. For this, they offered to flout the image of Jesus Christ and Mother of God, and this ritual they had to go through to the mid-nineteenth century. In General, Christianity was prohibited in Japan for two and a half centuries during this time were executed, tortured or deported thousands of people who professed this religion.

February 5, 1597 at Nagasaki were publicly executed for missionary activity 26 people, including 20 Japanese, four Spaniards, as well as Mexican and Indian. By order of the reigning shogun Toyotomi Hideyoshi the arrested Christians were tortured and then brought to Nagasaki and crucified on crosses installed on the hill of Nishizaka. After the execution of martyrs came to be revered as saints and recognizing that they have a variety of wonderful acts. One hundred years after their canonization in 1962 on the hill have opened a monument and a Museum. On 6 February, the Catholic Church in Japan celebrates their memory.

In the collection of the Museum contains important historical documents brought from Europe and made in Japan, works of art of the early period of Christianity in Japan. Exposure in chronological order acquaint visitors with the period of early Christianity, and at times persecution of Christians and the secret life of Catholics in the period of self-isolation.

Currently Christianity is the third major religions in Japan after Buddhism and Shinto. In the beginning of XXI century there were about 2, 5 million Christians, mostly Catholics.