The newly formed Society of Jesus led the way in missionizing Asia in the early modern period. The Jesuits cultivated regional Asian elites in an effort to accommodate Christianity with indigenous cultural elements. While Jesuit accommodation was criticized by other missionaries, it is clear that some process of inculturation (assimilation) was necessary for the long-term viability of Christianity in Asia.
In China, led by the pioneering Father Matteo Ricci (1552–1610), the Jesuits developed a mission strategy focusing on the scholar-officials. A number of prominent literati were converted in the early seventeenth century, including the famous Three Pillars of the Early Christian Church: Xu Guangqi (1562–1633), Li Zhizao (1565–1630), and Yang Tingyun (1557–1627). Instead of syncretizing the traditional Three Teachings (Buddhism, Confucianism, and Daoism), Xu proposed to "supplement Confucianism and displace Buddhism" by blending Confucianism and Christianity. This formula influenced later literati, such as Shang Huqing (b. 1619) and Zhang Xingyao (b. 1633). However, with the Manchu conquest of 1644, Chinese culture became more conservative and less open to creative synthesizing, causing the literati converts to decrease both in numbers and eminence.
In south India, a Jesuit named Robert de Nobili (1577–1656) studied the languages of ancient India (Sanskrit and classical Tamil) to develop a new and fruitful approach to inculturating Christianity into Tamil culture in the years 1605–1656. However, the Hindu and Muslim cultures of this region resisted Christianity, making South Asia far less fertile territory than East Asia. In southeast Asia, Buddhist cultures resisted the penetration of Christianity, with the notable exception of Vietnam. The French Jesuit Alexandre de Rhodes (1593–1660) developed a remarkably effective missionary method by creating a Vietnamese group of catechists who were trained in basic medicine and who lived as a celibate brotherhood. This led to the creation of a thriving Catholic Church. In more recent times, evangelical Protestants in Vietnam have grown to an estimated 700,000 in number.
In Japan, missionaries met with striking initial success followed by rejection. The Jesuit Francis Xavier arrived in 1549 while Japan was emerging from a period of warring feudal chaos, which provided a brief window of opportunity for the missionaries. Within sixty-five years, there were 300,000 Christians in a Japanese population of twenty million. However, fears of subversion by this foreign religion led to a harsh persecution of Christians that culminated in the death of 3,125 Christian martyrs in the years 1597–1660. Christianity was exterminated in Japan, except for a small group of underground Christians in the area of Nagasaki. Christianity never again rekindled the interest that it had in the late sixteenth century in spite of the extensive investment of American missionaries and church funds made in Japan in the aftermath of World War II.
The isolation of Korea, which was controlled by China, delayed the development of Christianity by denying access to missionaries. However, Jesuit publications in Chinese did reach China and these stimulated a young Korean named Lee Sunghun (1751–1801) to travel to Beijing and be baptized in 1784. Lee returned to Korea and converted other Koreans. The first Protestant missionaries entered Korea in 1885 and in the twentieth century, Korea became a leading area of Christian growth in Asia.
The entire population of the Philippines was converted within one century after the arrival of Spanish missionaries in 1565. Protestant missionaries first entered the Philippines when the Americans replaced the Spaniards as colonizers in 1898. The Philippines remain today the only Asian country where Christianity is a majority religion, although there has been rapid growth in China, Indonesia, Singapore, and South Korea.