French photographer Jean-Marc Bouju's picture topped a record 63,093 entries submitted to the 47th annual contest by 4176 photographers from 124 countries.
In the winning image, jagged wire partly obscures the view of the barefoot boy being comforted by his father, both seated on the sandy ground of a POW camp near Najaf in Iraq.
The man, dressed in white, was made to wear a black plastic hood by the US troops who detained him.
Shots of the war in Iraq dominated the news categories in the 2003 contest. Liberia, the Middle East and the Bam earthquake in Iran also provided images that told whole stories.
Reuters photographers Ahmad Jad Allah and Jerry Lampen both won prizes.
Jad Allah's picture of a raid on the Jabalya refugee camp in the Gaza Strip snatched a first for Spot News Singles.
Second prize: An Iranian in Bam
carries his sons to the cemetery
Lampen came first in General News Singles for his haunting image of a woman mourning her husband in Gaza.
The wailing woman, her face illuminated, has the quality of an oil painting.
Contest judge Ruth Eichhorn, photography director at GEO Germany, said the 2003 top award was given to Bouju because of the graphic and symbolic appeal of his father and son picture.
"It shows the suffering of the people in a very complicated war. It's not important who the man is. It's not important who made him wear the hood. The image, with the barbed wire, is symbolic," said juror Ruch Eichhorn.
"It's very graphic. I don't think these plastic hoods have been used much before and so the image looks quite scary but it also shows love. Love of the man for his son."