The president said the US must not repeat the mistake of backing repressive forces.
Mr Clinton, at a roundtable discussion with Guatemalan citizens, said that any US support given military forces or intelligence units that engaged in "violent and widespread repression" was wrong. "And the United States must not repeat that mistake," he said.
About 200,000 people died or disappeared during the Guatemalan civil war from 1960 to the mid-1990s.
Many deaths blamed on the US
BBC correspondent Clive Myrie, who is travelling with Mr Clinton, said his comments did not amount to the full-scale apology some were hoping for, but it is the closest any US President has come to acknowledging Washington's role in Guatemala's recent violent past.
Just last month an official Truth Commission in Guatemala blamed most of the thousands of deaths there during its civil war on the military government, which was backed by the US.
The president is on the final stage of his tour of Central America. Earlier, in an address to the Congress in El Salvador, he praised the return to democracy in Central America.
![[ image: width=150]](/olmedia/290000/images/_294663_clinton150.jpg)
Speaking in the capital San Salvador on the third day of his visit to the region, Mr Clinton said the Central American countries had often suffered from man-made disasters that were more cruel than those caused by nature.
For much of the 1970s and 1980s Central America was a battleground for competing factions during the cold war, with America often backing right-wing military regimes against leftist rebels.
Mr Clinton did not, as many had hoped, apologise for the US role in what he called a brutal past but he did say he hoped the people of this region now saw his country in a new light, as a partner and friend.
In talks with Salvadoran President Armando Calderon ahead of his speech, Mr Clinton was urged to reverse US policy on deporting thousands of illegal immigrants back to the region.
'We must enforce our laws'
President Calderon, who has fought against US deportation throughout his five-year term which ends in June, made his case in a 30-minute meeting.
Before their talks, President Calderon said: "We hope that legal status can be granted to those who do not have it and we believe that if this does not happen, then the human rights of these immigrants would be violated."
But Mr Clinton responded to El Salvador's fears that some half a million of its citizens would be sent home from the United States by telling the El Salvador Congress: "We must enforce our laws, but we will do so with justice and fairness."
President Clinton also repeated promises of close to one $1bn of US aid for the region.
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(10 Mar 99 | Americas)
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The White House
Washington Office on Latin America
Offcial site of the El Salvador President (in Spanish)
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