The returnees, who arrived in Bor by ferry on Sunday, were part of about 4,800 IDPs who had been staying at UNHCR's Lologo way station near Juba, UNHCR spokesman Mans Nyberg said.
"Sixteen years ago, as the ravages of the civil war reached their home region, these Dinkas fled Bor and settled around Maridi in Western Equatoria State," he added.
Nyberg said Sunday's movement was the first of 12 ferry trips planned for the next two months.
Southern Sudan was until recently engulfed in 21-year a war between the former rebels of the Sudan People's Liberation Movement/Army and the Khartoum-based government.
The war displaced about four million people and forced another 550,000 to flee to neighbouring countries.
"The signing of the peace agreement in January 2005 finally created the possibility for them to return to Bor," Nyberg said. "After the end of the rainy season in November last year, they started to return on foot."
"With their half a million head of cattle they crossed the White Nile at Juba, and continued north along the east bank of the river," he added. "That trek is still going on; 250,000 cattle have arrived so far and are now in 34 cattle camps around Bor."
He said a second group of 4,600 Dinkas from Bor, displaced in December to Yei, would be assisted to return once all the IDPs from Juba were back. The Yei group fled inter-ethnic conflict in Western Equatoria, where they had been displaced until then.
UNHCR has established a way station at Bor where the UN World Food Programme, the UN Children's Fund and the Adventist Development and Relief Agency International are providing returnees with food, medicine and medical care.
"The general situation in Bor remains difficult, with very little infrastructure and few services," Nyberg said. "Many villages in the surrounding countryside are hard to reach because of landmines in roads and fields."
"Despite these challenges, the only wish of the IDPs in Juba and Yei is to return home," he added.