US doctors say the discovery could explain why babies lying face down are more likely to die, because in that position their reflexes are harder to trigger if they have trouble breathing.
"These findings provide evidence that SIDS is not a mystery but a disorder that we can investigate with scientific methods, and some day, may be able to identify and treat," said Hannah Kinney, senior author of a study published in Wednesday's issue of the Journal of the American Medical Association (JAMA).
Neurologists Kinney and David Peterson of Children's Hospital Boston and
Harvard Medical School, in Massachusetts, examined the brains of 31 babies who died from SIDS and 10 others who died from other causes.
They focused on the brainstem in the lower part of the brain where they found abnormalities in nerve cells that use and recycle serotonin, a brain chemical that plays a role in communications between brain cells.
The researchers believe serotonin and the brainstem cells that produce it help regulate breathing, blood pressure, sense carbon dioxide (CO2) levels and body temperature.
"Our goal is to find a way -- a diagnostic test -- to identify these defects in living infants and then find a way to correct these defects by drugs or other means as the infant passes through the first six months of life, the period of greatest risk for SIDS," Dr Kinney said.
When a baby sleeps on its stomach, face down on a pillow, or with its head covered by a blanket, it breathes less oxygen and more CO2.
Normally, increased CO2 levels trigger nerve cells in the brainstem that stimulate respiration and alertness centres in the brain to prevent the baby's suffocation, the researchers said.
A normal baby would wake up in such circumstances, Dr Kinney said, but for those with abnormalities in their serotonin-producing mechanisms the respiratory and waking reflexes may be impaired, she added.
SIDS is the leading cause of death among babies three weeks to five months of age, with a mortality rate of 67 per 100,000.