In 1975 Pol Pot concluded an alliance with the party head of the Southwestern Zone, Ta Mok, who was a Khmer Issarak veteran and, like Pol Pot, was strongly anti-Vietnamese. During 1977 and 1978, Ta Mok provided the backing that enabled Pol Pot to liquidate the opposition within the KCP and to initiate new terrorism against the local population. In February 1977, Southwestern cadres went into the Eastern, Northern, and Western zones to purge local Khmer Rouge. Four months later, the same process was begun in the Northwestern Zone. The purges intensified following an abortive coup d'état in August.

After the fall of the capital, Ta Mok's lieutenant, a former high school teacher who assumed the name Mit (Comrade) Deuch, became head of the secret police, and established the Tuol Sleng interrogation and detention center on the site of a former Phnom Penh high school. In the 1975 to 1976 period, Tuol Sleng's meticulous records show that 2,404 "antiparty elements" were tortured and executed. The terror escalated in 1977, when the number of victims rose to 6,330. In the first six months of 1978, records show that 5,765 people were killed records for the latter half of that year have not been discovered. The victims who passed through Tuol Sleng from mid-1975 to January 1979 numbered about 20,000. Among those who met death in the infamous prison were Paris alumni Hu Nim and (presumably) Hou Yuon. Similar centers were set up throughout the country (Tuol Sleng's code designation, S-21, suggests that at least twenty other similar sites had been established). Molyda Szymusiak writes that a new wave of terror began in the Batdambang region after cadres arrived from the south. The Sala Som Niat, a school for political education was converted into an extermination center where local communists were tortured and executed. The pattern in these centers was much the same: victims were tortured, forced to write often absurd confessions, and then killed. A young British teacher, captured in a yacht off the Cambodian coast, confessed at Tuol Sleng that he had been recruited by the Central Intelligence Agency (CIA) of the United States when he was twelve years old he was subsequently murdered. Hu Nim was forced to confess that he had become a CIA agent in 1957.

The Eastern Zone apparently remained largely unaffected by the purge until May 1978, when So Phim led a revolt that provoked massive retaliation by Pol Pot and his Southwestern henchmen. In the bloodiest purge of the entire 1975 to 1978 period, as many as 100,000 people in the Eastern Zone--labeled people with "Khmer bodies but Vietnamese minds"--were liquidated or were deported to face certain death in other parts of the country. Most of the victims were political cadres, "new people," and Vietnamese or part-Vietnamese residents. So Phim reportedly committed suicide as he faced capture. Some of his subordinates, including Heng Samrin, the leader of the PRK after 1979, fled to Vietnam.

Data as of December 1987