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The first Europeans to Japan came from Portugal and landed on Kyushu in western Japan in 1542, bringing both gunpowder and Christianity along with them. Some lords, especially on Kyushu, and Japan's upcoming leader Oda Nobunaga welcomed these new visitors for the weapons they brought with them and tolerated the missionaries that came together as part of the package.

The missionaries were eventually successful in converting considerable numbers of people in western Japan, including members of the ruling class. Christianity could be practiced openly, and in 1550, Francis Xavier undertook a mission to Kyoto to seek an audience with the Emperor.

However in 1587, in an era of European conquest and colonization, including in the Philippines near Japan, Toyotomi Hideyoshi issued an edict banning missionaries from the country due to the religion's political ambitions, intolerant behavior towards Shinto and Buddhism, and connections to the sale of Japanese people as slaves overseas. In 1597, Hideyoshi proclaimed a more serious banning edict and executed 26 Christians in Nagasaki as a warning.

Intent to bring Japan under complete control, the succeeding Tokugawa Shogunate further hardened the country's anti-Christian stance, accusing the religion of obstructing the authorities, antisocial behavior and intolerance towards the established religions. After a rebellion on the Shimabara Peninsula that involved many Christians in the late 1630s, thousands of rebels were executed and a full ban on Christianity became strictly enforced. Only small pockets of Christians, known as the "Hidden Christians", continued practicing their religion in secret.

Following the Meiji Restoration, freedom of religion was promulgated and the number of Japanese Christians has been slowly increasing again. Today, about one to two million Japanese are Christians (about one percent of Japan's population), and churches can be found across the country. Many Christians live in western Japan where the missionaries' activities were greatest during the 16th century.

A few Christian customs that have become popular among the non-Christian population in modern-day Japan include Christian-style wedding ceremonies, at which brides wear white wedding dresses and the couple exchange their vows at wedding chapels.

Events like Valentine's Day and Christmas have developed secular status, and retail marketing for these celebrations contribute to their popularity. Seasonally appropriate gifts and decorations start lining the shelves weeks in advance, and illumination events are held. Note that while commonly celebrated by the populace, Valentine's Day and Christmas are not national holidays in Japan.

The following is a list of tourist sites related to Christianity in Japan:

Amakusa Islands

Shitsu Church and Ono Church

Sasebo

Kuroshima Church

Goto Islands

Tsuwano Catholic Church

Saint Nicolai Church

Stone Church

Christ's Grave