It is more likely however, historically speaking, that Chan began to develop gradually in different regions of China as a grass-roots movement which was reacting to what was perceived as an imbalance in Chinese Buddhism towards the blind pursuit of textual scholarship with a concomitant neglect of the original essence of Buddhist practice—meditation and the cultivation of the right view. After the time of Huineng, Chinese Chan began to branch off into numerous different schools, each with its own special emphasis, but all of which kept the same basic focus on meditative practice, personal instruction and grounded personal experience. During the late Tang and the Song periods, the tradition flowered, as a wide number of eminent teachers such as Mazu 馬祖, Baizhang 百丈, Yunmen 雲門 and Linji 臨濟 developed specialized teaching methods that would become characteristic in each of the 'five houses'  五家 of mature Chinese Chan.

Later on, the teaching styles and words of these classical masters were recorded in such important Chan texts as the Biyan lu 碧巖錄 (Blue Cliff Record) and the Wumen guan 無門關 (Gateless Barrier), which would be studied by later generations of students down to the present. Chan continued to be influential, along with Pure Land 淨土 as a Buddhist religious force in China, although some energy was lost with the revival of Confucianism 宋學 from the Song onward. Chan was mostly eliminated in China in the modern era with the appearance of the Peoples Republic, but still continues to hold a significant following in Taiwan.

Chan was gradually transmitted into Korea during the late Silla period (8th and 9th) centuries) as Korean monks who came from a predominantly Hwaeom 華嚴 and Consciousness-only 唯識 background began to travel to China to learn the newly developing tradition. The first transmission of Chan into Korea is attributed to a monk named Beomnang 法朗, but he was soon followed by a throng of Seon students, who later returned to Korea to establish the 'nine mountain'  九山 schools, with 'nine mountains' becoming a nickname for Korean Seon which survives down to the present. Korean Seon received significant impetus and consolidation from the Goryeo monk Jinul 知訥, who established the Songgwangsa temple 松廣寺 as a new center of pure practice. It is from the time of Jinul that the Jogye 曹溪 became the predominant single meditative school in Korea, surviving down to the present retaining basically the same status. Toward the end of the Goryeo and during the Joseon period the Jogye school would first be combined with the scholarly gyo 教 schools, and then suffer from persecution at the hands of a Confucian influenced polity. Nonetheless, there were a number of important teachers who appeared during the Joseon, including, such as Hyegeun 慧勤, Taego 太古, Gihwa 己和 and Hyujeong 休靜, who continued to develop the basic mold of Korean meditative Buddhism established by Jinul. The Seon tradition, in the form of the Jogye school 曹溪宗, presently constitutes the predominant form of Buddhism in Korea, and Seon continues to be practiced in Korea today at a number of major monastic centers.

Despite the fact that Japanese Buddhists were aware of the development of the Chan school in China from a fairly early date, no formal schools were established until the 12–13th centuries, when Eisai 榮西 and Dōgen 道元 established the Rinzai 臨濟 and Sōtō 曹洞 schools, respectively. The Zen movement in Japan was fortunate to receive the patronage of the growing new force in Japanese politics, the military bakufu 幕府, and so both schools developed and throve for several centuries. But although the Shogunate of the Edo period supported Zen as an official religion, tight government control of the school limited its creativity. Nonetheless, the Japanese schools of Zen produced a number of significant creative teachers, including such figures as Ikkyū 一休, Bankei 盤珪 and Hakuin 白隱. There are still a number of famous Zen monasteries preserved to the modern day in Japan, although the number of actual practicing Zen monks has declined sharply.

Although there is good reason to speak of the 'Zen school' as a distinct branch of the Buddhist tradition of Japan, there has never been any organized social or institutional entity bearing that name. At present, there are twenty-two comprehensive religious corporations 包括宗教法人 registered with the Japanese government that are recognized as belonging to the Zen tradition 禪系. These include: the Sōtōshū 曹洞宗; fifteen separate corporations that identify themselves as branches 派 of the Rinzaishū 臨濟宗; the Ōbakushū 黃檗宗; and five small corporations that have splintered off from the Sōtō and Rinzai organizations. Each of the twenty-two Zen denominations has a number of temples affiliated with it, ranging from 14,664 in the Sōtō school to 3,389 in the Myōshinji branch of the Rinzai school 臨濟宗 妙心寺派, 455 in the Ōbaku school, a few hundred in the smaller Rinzai denominations, and just a handful in the smallest of the corporations (all data from Bunkachō 文化廳, ed., Shūkyō nenkan 宗教年鑑, 2003 Edition).

One thing that clergy affiliated with all the Zen denominations in Japan hold in common is the belief in a Zen lineage 禪宗 of Dharma transmission said to have been founded by the Buddha Śākyamuni, established in China by the Indian monk Bodhidharma, and subsequently transmitted to Japan by numerous Japanese and Chinese monks. During the Kamakura period (1185–1333) and the two decades immediately following, by one account, some twenty-four separate branches 流派 of the Zen lineage were established in Japan. By another reckoning, there were forty–six individual transmissions of the Zen dharma to Japan, beginning with Myōan Eisai 明庵榮西 (1141–1215) in 1191 and extending down to the Chinese monks Yinyuan 隱元 (1592–1673) and Xinyue 心越 (1639–1696), a dharma heir in the Caodong Lineage following Wuming Huijing 無明慧經 (J. Mumyō Ekyō; 1548-1618), came to Japan in 1677 and established the Jushō Branch (C. Shouchangpai 壽昌派; J. Jushōha) of the Sōtō Lineage, which was based in Mito Domain 水戸藩.. At present, however, all Zen clergy trace their own lineages of dharma inheritance back to China through only two men: (1) Nanpo Jōmyō 南浦紹明 (1235–1308), a.k.a. Daiō Kokushi, founder of the Daiō branch 大應派 of Rinzai Zen; and (2) Dōgen Kigen 道元希玄 (1200–1253), founder of the Dōgen branch 道元派 of Sōtō Zen. All the other branches of the Zen lineage that flourished in the past are said to have died out, having failed at some point to produce any more dharma heirs. See 'Zen lineage.'

Most of the Zen denominations in Japan operate training monasteries in which the bureaucratic structures, ritual calendars, and modes of practice are modeled after those found in the leading Buddhist monasteries of Song (960–1279) and Yuan (1280–1368) dynasty China. Those institutional forms were first imported into Japan in the Kamakura period, chiefly (but not exclusively) by the same monks who transmitted the Zen lineage. Texts containing the religious lore of the Zen lineage in China — genealogies of Dharma transmission, biographies of Zen masters, records of their discourses, and kōan collections — were also brought to Japan at that time, and have been handed down to the present within the various denominations as the common heritage of the Zen school.