Northern Alliance fighters beat up Taleban prisoners
After the capture of the city, an alliance commander, General Abdul Rashid Dostum, said the rights of some 6,000 Taleban fighters who had surrendered would be respected.
But there have been reports of Taleban prisoners being beaten and shot dead in the marketplace.
Fly-covered bodies of Taleban lay strewn in the city's streets, some with their big toes tied together as proof that they had no chance of escaping brutal death.
Residents walked by the bodies and stared, but nobody touched or removed them.
Breach of agreement
There was also looting.
Northern Alliance soldiers drove through the city, towing pick-up trucks they said had belonged to Taleban.
Earlier, Northern Alliance soldiers had gone from house to house, searching for hiding Taleban fighters.
Those who surrendered were taken away in trucks, their hands tied behind their backs.
If the Taleban fighters were indeed beaten and shot dead, as residents have testified, this would be a breach of an agreement reached with the Taleban in Kunduz, according to which Afghan Taleban fighters would be given amnesty.
Foreign fighters, including Pakistanis, Chechens and Arabs were to be imprisoned and tried.
Fate of foreigners
But the foreigners have suffered brutal treatment at the hands of Northern Alliance forces during their takeover of other Afghan cities in recent weeks, and there is concern that they will meet a fate worse than the Afghans they fought with.
Former Afghan President Burhanuddin Rabbani said that Northern Alliance troops would not "injure or harass" the foreign fighters in Kunduz.
"Although they have committed some war crimes in Afghanistan, they come under the general amnesty that we have declared and they will be pardoned if they put their guns down," Mr Rabbani said.
He added that those captured could be handed over to the United Nations.