The revelation raises serious questions about the legacy of more than 10 years of western involvement in Afghanistan.
"After the age of two years, stunting is largely irreversible, and has an impact on growth and development and cognitive function," says Carrie Morrison from the World Food Program.
"Over the longer term, it can have a very damaging effect on the national economy. Young people are not able to attain what they should be able to attain. Women who marry young and are stunted themselves give birth to a small infant and the cycle goes on."
The problem of children who are not getting enough nutrients from their food is known as chronic malnutrition. It afflicts poorer countries worldwide, but in Afghanistan it is particularly widespread and persistent.
The malnutrition problem is caused by the basic poverty of those who can't afford healthy food, as well as poor hygiene and healthcare, child marriage, and a web of other issues.
"We have whole families where food insecurity means they are all malnourished, but we [also] even have rich families that have one child who is sick," says Alam Mohammad, a 25-year-old doctor who swapped the chance of an easy city practice to work in Feroz Nakhchair, on the grueling frontline of a fight for the country's future.
Extreme poverty and a harsh climate mean many Afghans go hungry. One-third of the population do not get enough food to live healthy, active lives, and another third hover around the borderline of "food insecurity", or not knowing where their next meal will come from. But the food shortages are particularly damaging to young children, who need to develop fast.
Overall malnutrition shaves 2%-3% off Afghanistan's national income each year, the World Bank says. That's around half a billion dollars lost to an already very poor country.
SHI/SHI