Charles heard from relatives of some of the 1,668 people still missing when he attended a meeting at the offices of President Atifete Jahjaga in Pristina.
He was in the capital with the Duchess of Cornwall for the last leg of their tour of the Balkans, a region torn apart by the conflict during which 4,500 people disappeared.
After laying a bunch of white roses at a memorial for the missing, the Prince and the Duchess greeted crowds of adoring well-wishers.
One woman, 55-year-old Elvane Dana, told the Prince 10 members of her family were taken (by the Serbs) – including her 16 and 18-year-old sons – from their home and that only eight had returned.
They were taken from Glakova on May 10, 1999, and almost 17 years later are still unaccounted for.
On hearing her story, the Prince leaned in to give her a hug, having been visibly moved by the plight of the families.
Taking a deep breath, and holding back tears, Ms Dana said: “I am so honoured. I have a special respect for the UK and we need all the help we can get.
“I am touched the Prince took the time to hear my story and that he so lovingly hugged me.”