The Northwestern University team had previously shown patients with back pain had decreased activity in the same brain region called the thalamus.
This area is known to be important in decision-making and social behaviour.
The team's current study in the Journal of Neuroscience suggests some of the changes may be irreversible and render pain treatment ineffective. More research is needed, they say.
Shrinkage
If true, it makes it all the more important to treat pain early to prevent any permanent change, say Dr Vania Apkarian and colleagues.
They scanned the brains of 26 patients with chronic back pain and 26 healthy people.
The patients with chronic pain caused by damage to the nervous system showed shrinks in the brain by as much as 11% - equivalent to the amount of gray matter that is lost in 10-20 years of normal aging.
The decrease in volume, in the prefrontal cortex and the thalamus of the brain, was related to the duration of pain.
Every year of pain appeared to decrease gray matter by 1.3 cubic centimetres.
What the researchers now need to find out is whether this loss is permanent or whether it can be reversed with treatment.
Dr Apkarian said: "It is possible that some of the observed decreased gray matter shown in this study reflects tissue shrinkage without substantial neuronal loss, suggesting that proper treatment would reverse this portion of the decreased brain matter."
Permanent loss?
But Dr Apkarian said other research in rats had shown that spinal cord neurons die, which suggests the brain changes could be irreversible.
Dr Nigel Lawes, senior lecturer in biomedical science at St Georges Medical School, London, said: "This is a very interesting study.
"Other imaging studies have shown in chronic pain conditions these areas of the brain are less active, so it does correspond with what other people have found."
He said the brain areas involved, which control decision making such as how to consciously move the body, might be important.
He said people with chronic back pain tended to move in automatic ways that perpetuate the pain.
Therapies to teach people how to pay attention to and control their movement to limit this pain might help, he said.
"Studies could look at whether any of these therapies improve the way they cope with their pain, do you reverse the underactivity in that part of the brain and, after you have reversed it for long enough, will that then change the brain volume?
"It might well be that it is reversible, but that depends on whether they get the right treatment or not."