The International Criminal Court has issued its first arrest warrants, for five leaders of the Ugandan rebel movement, the Lord's Resistance Army.
The LRA is notorious for child abductions
No names have been revealed, but the leader of the LRA, Joseph Kony, is believed to be among them.
The LRA is accused of widespread murder and torture during nearly 20 years of fighting against the army. They have kidnapped thousands of children.
Human Rights Watch welcomed the move as an "historic development".
"It stamps the accused... as indicted war criminals by an international court. That has not happened before," International Justice Programme director Richard Dicker said.
The BBC's Will Ross in Kampala says the arrest warrants will put an end to peace talks.
Many northern Ugandans had hoped negotiations would solve the conflict, in which thousands have been killed and 1.5 million people forced from their homes.
Uganda asked the Hague-based court to investigate violations in northern Uganda last year.
The request was the first time a state had asked the court to take up a case.
The head of the UN mission in the Democratic Republic of Congo told a news conference the Ugandan government had been informed of the warrants.
INTERNATIONAL CRIMINAL COURT
First permanent court to try individuals for genocide, war crimes and other human rights violations
Rome Statute set up in July 1998, when 120 countries adopted the treaty
Came into force in April 2002 after ratification by 60 countries
Uganda and DR Congo investigations began in 2004
Inquiry in west Sudan's Darfur region began in 2005
William Swing said Congo and Sudan, where some of the rebels are based, had also been notified.
The LRA are known for abducting young children, to become fighters or sex slaves.
Human rights groups also accuse them of murder, mutilation, torture and rape.
"Victims have been suffering at the hands of the LRA for near... 20 years in northern Uganda," Mr Dicker said.
But he added that he hoped the court would also investigate the Ugandan army, which is also accused of abuses against civilians during its war with the rebels.
The Ugandan ambassador to the US, Edith Sesempala, welcomed the news, saying the arrests would be good for peace and human rights in northern Uganda.
Earlier this year some Ugandans expressed fears that such a move could derail negotiations between the LRA and the government.
Ugandan civilians live in constant fear of attacks
Under an amnesty, for the past few years rebels who come out of the bush and gave themselves up were free from prosecution.
And the peace talks, backed by several Western countries, produced a historic face-to-face meeting between government ministers and senior LRA rebel commanders last year.
However, diplomats at the UN have suggested that the peace effort may have run its course.
Observers accuse both sides of not putting enough effort into negotiating an end to the war, our correspondent says.
Ugandan President Yoweri Museveni has favoured a military approach, but this has so far failed to bring about a lasting peace and the LRA continues to target civilians.
On Thursday, Ugandan military spokesman, Lieutenant Colonel Shaban Bantariza, announced that Sudan has given permission to the Ugandan army to pursue LRA fighters into its territory beyond the 120km limit already agreed.
The big question now, our correspondent says, is how the LRA commanders will be arrested in order to face justice.