After the introduction of Christianity to Japan in 1542, the religion enjoyed some popularity especially in the areas around today's Nagasaki Prefecture. However, the religion's aggressive and intolerant aspects eventually brought it into conflict with the Japanese leaders who ultimately banned Christianity during most of the Edo Period (1603-1867) and persecuted missionaries and believers.

Some local devotees, known as the hidden Christians, went into hiding in remote areas and on isolated islands where they continued practicing their religion secretly for over two centuries. Some sites pertaining to these hidden Christians survive today, including churches that were built after the ban on Christianity had been lifted in the early Meiji Period.

A number of these churches and sites received World Heritage status in summer 2018. They are shown on the map and described in the list below:

  • Oura Cathedral
  • Sotome
  • Kuroshima Church
  • Hara Castle Ruins
  • Hirado Island
  • Goto Islands
  • Sakitsu Village