The UN rights office said it was "deeply concerned" over the "zero tolerance" policy introduced by the administration of US President Donald Trump in a bid to deter illegal immigration.
Spokesperson Ravina Shamdasani warned the US policy had "led to people caught entering the country irregularly being subjected to criminal prosecution and having their children - including extremely young children - taken away from them as a result."
She said information received from US civil society groups indicated that several hundred children had been separated from their parents at the border since October, including a 1-year-old.
"The US should immediately halt this practice," she told reporters in Geneva.
"The practice of separating families amounts to arbitrary and unlawful interference in family life, and is a serious violation of the rights of the child," she said.
"The use of immigration detention and family separation as a deterrent runs counter to human rights standards and principles," she said.
Shamdasani stressed that children's rights were "generally held in high regard" in the US, but she lamented that the country was the only one in the world that had not yet ratified the UN Convention on the Rights of the Child.