The Vietnamese government maintains far-reaching control of religious activities and organizations through the process of recognition and registration, with unregistered religious activity illegal. In its May 2007 report the US Commission on International Freedom (USCIRF) cited continued arrests of individuals because of their religious activities and severe religious freedom restrictions targeting some ethnic minority Protestants and Buddhists, Vietnamese Mennonites, Hao Hoa Buddhists, and monks and nuns associated with the Unified Buddhist Church of Vietnam. USCIRF recognized some positive religious freedom developments in Vietnam, such as releasing prominent religious prisoners. However, since Vietnam joined the World Trade Organization, positive religious freedom trends have, for the most part, stalled, and Vietnam has initiated a severe crackdown on many religious leaders.

After the fall of Saigon, Montagnard (or Degar) guerrillas continued a separatist campaign in Vietnam's Central Highlands until the early 1990s, when they disbanded, put down their arms and took up Christianity. Vietnamese authorities have declared the form of evangelical Christianity followed by many Montagnards a political movement, not a religion, and made it illegal. According to the Montagnard Foundation, in 2007 Vietnam has continued to prevent human rights monitors from having unhindered access to the Central Highlands. Over 350 Montagnard prisoners of conscience remain in Vietnamese prisons under brutal conditions.

Minority and indigenous groups continue to be displaced from their ancestral lands in the name of development in Vietnam. In the highlands in the north, the International Rivers Network reports that close to 100,000 people belonging to 13 indigenous groups may be resettled under a programme which began in December 2005 and is expected to be completed by 2015 (1,000 families had been moved by the end of 2006) in order to make place for the Son La Hydropower Project, which is the largest dam project ever built in Vietnam.

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