Only the first two Heian emperors were much involved in governing. By 860 political management had been taken over by a series of regents from the Fujiwara family, who supplied most of the empresses in this period. The emperors continued to be honored, even venerated, because of their presumed divine descent, but the Fujiwaras ruled. Fujiwara dominance represented the privatization of political power and a return to clan politics. Political history thus took a very different course in Japan than in China, where, when a dynasty weakened, military strongmen would compete to depose the emperor and found their own dynasties. In Japan for the next thousand years, political contenders sought to manipulate the emperors rather than supplant them.

The Fujiwaras reached the apogee of their glory under Fujiwara Michinaga (r. 995–1027). Like many aristocrats of the period, he was learned in Buddhism, music, poetry, and Chinese literature and history. He dominated the court for more than thirty years as the father of four empresses, the uncle of two emperors, and the grandfather of three emperors. He acquired great landholdings and built fine palaces for himself and his family. After ensuring that his sons could continue to rule, he retired to a Buddhist monastery, all the while continuing to maintain control.

By the end of the eleventh century several emperors who did not have Fujiwara mothers had found a device to counter Fujiwara control: they abdicated but continued to exercise power by controlling their young sons on the throne. This system of rule has been called cloistered government because the retired emperors took Buddhist orders, while maintaining control of the government from behind the scenes. Thus for a time the imperial house was a contender for political power along with other aristocratic groups.