The violent protests in Tibet that began last week and have since spread across (and beyond) China are frequently depicted as a secessionist threat to Beijing. But the regime's deeper problem in the current crisis is neither ethnic nor territorial. It's religious.

If there's a template for Beijing's policy on religion, it's the "Invasion of the Body Snatchers." In 1995, the regime effectively kidnapped Gendun Choekyi Nyima, a 6-year-old boy named by the Dalai Lama as the 11th Panchen Lama, the second-highest ranking figure in Tibetan Buddhism. In Nyima's place, Beijing designated its own "official" Panchen Lama, the slightly younger Gyaltsen Norbu. Nyima's whereabouts, assuming he's alive, are unknown. More recently, a new set of "implementation regulations" on Tibetan religious affairs has come into force, drastically curtailing the freedom of monks and nuns to travel within China, and introducing political themes into the qualification exams required of religious initiates. Of the roughly 100 Tibetan political prisoners, fully three-quarters are monks or nuns.

Much the same goes with China's Christians. The regime has substituted its own Catholic hierarchy -- the Catholic Patriotic Association -- for Rome's since 1957, leading to endless friction between the Pope and the Communist Party. Similarly, Chinese Protestantism officially operates under the so-called "Three-Self Patriotic Movement" (the three "selfs" being self-governance, self-support and self-propagation), which in turn is regulated by the party. "The purpose of [the regime's] nominal degree of sympathy for Christianity is to indoctrinate and mobilize for Communist Party objectives," says journalist David Aikman, author of the 2003 book "Jesus in Beijing." "I've often joked that the most leftist people in China are members of the Three-Self Church."

The method here is not subtle. The regime banned religion -- one of the so-called Four Olds -- during the Cultural Revolution. Once it figured out that that didn't work, it sought instead to turn clergy into bureaucrats, and replace the idea of the divine with the mechanics of political control. The results have been, at best, a partial success. There are now some six million "Catholics" who adhere to the state-approved dogma, along with another 20 million or so "official" Protestants, whose activities are overseen by a director of the State Administration for Religious Affairs. As for Tibetan Buddhists, those who venerate the state-approved Panchen Lama can probably be counted on the fingers of one hand.

By contrast, the number of underground Catholics faithful to the Vatican easily equals the number of official ones. Unofficial Protestants, who attend unsanctioned "house churches," are said to number anywhere between 70 million and 130 million; one prominent Chinese pastor puts the count closer to 300 million. That latter figure is probably exaggerated, but there's no question that Christianity of the unofficial kind is winning Chinese converts in huge numbers. Not only that, it's winning them among every class of Chinese: farmers, urban migrant workers, professionals and intellectuals.

What is the appeal of Christianity to so many Chinese -- or, for that matter, of Buddhism, Taoism, Islam, the old-time peasant religions and the newfangled Falun Gong? In "smashing" organized religion, Mao Zedong also destroyed the traditional institutions of charity and social support that used to provide succor to the lonely and the needy. Now that succor is desperately in demand, and the churches are there to meet it.

The party also helped destroy traditional morality in the name of an ideology it has itself largely abandoned. To a degree that alarms even Chinese rulers, morality and ideology have been replaced by corruption, opportunism and widespread indifference to life's ordinary decencies. Religion offers a corrective to this, too, as it does to the quandaries of 21st century existence. "A lot of urban people have challenges in their lives," says Mr. Aikman. "Professional challenges, divorces; all sorts of things that didn't exist 15 years ago are now requiring people to ask very serious questions about the way they lead their lives."

Just as remarkable is how all this is slipping beyond Beijing's grip. The repression of Tibetan Buddhists and the Falun Gong has been severe, mainly because both dared to challenge the Party directly. Most Christians pose no such obvious challenge, particularly Protestants who belong to no formal organization, have no connections to outsiders, and do not openly question government policy. Some party leaders even see Christians as model citizens, patriotic even if they are not members of a "patriotic association."

Yet precisely because the party's captains and engineers tend to assess threats and opportunities in purely utilitarian terms, they tend to miss the real threat that a religious revival poses to their power. As French essayist Guy Sorman notes in his brilliant book "Empire of Lies," religion operates "in the realm of beliefs and conscience, where the party has no control." Mr. Sorman, who spent the year of the rooster (2005) traveling the length and breadth of China, recalls that one religious uprising, the 19th-century Taiping rebellion, destabilized the Manchu Dynasty, which in turn was succeeded by the Republic of Sun Yat-Sen, a Christian.

Might the same happen again in China? Nobody can say. But on the streets of Lhasa, China has again had a vivid demonstration of the power of conscience to move people to action against a soulless, and brittle, state.