In the aftermath of the San Felipe incident of 1596, 26 Catholics – four Spaniards, one Mexican, one Portuguese from India (all of whom were Franciscan missionaries), three Japanese Jesuits, and 17 Japanese members of the Third Order of St. Francis, including three young boys – were executed by crucifixion in Nagasaki on the orders of Hideyoshi Toyotomi on February 5, 1597.
These individuals were raised on crosses and then pierced through with spears.

After the persecution of 1597, there were sporadic instances of martyrdom until 1614, in all about 70.
55 Catholics were martyred in Nagasaki on September 10, 1632, in what became known as the Great Genna Martyrdom.
At this time Catholicism was officially outlawed.
The Church remained without clergy and theological teaching disintegrated until the arrival of Western missionaries in the 19th century.

Shūsaku Endō's acclaimed novel Silence, drawn from the oral histories of Japanese Catholic communities, provides detailed accounts of the persecution of Catholic communities and the suppression of the Church.
In the aftermath of the San Felipe incident of 1596, 26 Catholics – four Spaniards, one Mexican, one Portuguese from India (all of whom were Franciscan missionaries), three Japanese Jesuits, and 17 Japanese members of the Third Order of St. Francis, including three young boys – were executed by crucifixion in Nagasaki on the orders of Hideyoshi Toyotomi on February 5, 1597. These individuals were raised on crosses and then pierced through with spears.
After the persecution of 1597, there were sporadic instances of martyrdom until 1614, in all about 70. 55 Catholics were martyred in Nagasaki on September 10, 1632, in what became known as the Great Genna Martyrdom. At this time Catholicism was officially outlawed. The Church remained without clergy and theological teaching disintegrated until the arrival of Western missionaries in the 19th century.
Shūsaku Endō's acclaimed novel Silence, drawn from the oral histories of Japanese Catholic communities, provides detailed accounts of the persecution of Catholic communities and the suppression of the Church.
26 Martyrs of Japan