Francis Xavier landed in Kagoshima, Kyūshū, in 1549, with gifts that included a musical instrument (a clavichord?), and established at Yamaguchi the first of a series of Christian churches in Japan. As the number of converts increased, provision was made to render the liturgy in Japanese and to train the Japanese in Western music, including both singing and instrumental playing; dramatized versions of Bible stories were also performed. By 1580 there were some 200 churches in western Japan, as well as two seminários and a colégio, founded by Alessandro Valignano (1539–1606). In 1579 Valignano brought a pair of organs from Goa, and these, as well as other keyboard and string instruments, were used in services and at the seminaries.
The highlight of the Jesuit mission was an embassy to Rome, planned by Valignano. Four samurai boys from Kyūshū, with escorts, left Nagasaki in February 1582, reached Lisbon in August 1584 and gradually made their way to Rome, attending masses and giving musical performances along the route. They were received by Felipe II of Spain, had an audience with Gregory XIII (Pope, 1572–85) and attended the installation of his successor, Sixtus V (Pope, 1585–90). They attracted attention everywhere, even having their portraits painted by Jacopo Tintoretto (1518–94). They finally returned to Japan in 1590, and the following year they were received by Toyotomi Hideyoshi (1536–98), whom they impressed with their ability in Western music. Over the next 20 years Christian missions in Japan were at their height, one achievement being the publication in Nagasaki of Manuale ad sacramenta ecclesiae ministrandum (1605), printed in red and black with many pages of musical notation. However, both Hideyoshi and his successor Tokugawa Ieyasu (1542–1616) became suspicious, particularly after the arrival of Dominican (1592) and Franciscan (1593) missionaries from Manila. After a series of persecutions, a general order in 1614 banned all missionary activity, and new, more intense persecutions followed in the 1620s and 30s. A definitive order of 1639 brought to an end this first period of Christianity and its music in Japan, all remaining missionaries and their converts being evacuated to Macao, Manila or elsewhere.