Researchers found the volume of the hypothalamus - an area about the size of an almond tended to be larger in those who were overweight.
The differences were most apparent in the regions that control the release of hormones to balance hunger and fullness.
It was unclear whether these structural changes were a cause or consequence of weight gain, experts from Cambridge University said.
They analysed MRI scans from 1,351 young people with a range of different weights.
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