Baffled, the medical examiner who conducted the autopsies reached out to researchers at the Mayo Clinic, who over the years were contacted about other Amish children who had died sudden deaths.
After years of searching finally last week researches at the Mayo Clinic lab were able to get answers, thanks to new technology which enabled them to finally pinpoint the cause.
The Mayo Clinic researchers discovered all the Amish children had the same genetic mutation, which they had inherited from their parents.
Twenty-three Amish children had inherited the mutation and only five hadn't died sudden deaths, results published in JAMA Cardiology revealed.
They discovered the reason for the deaths was a particular mutation of the gene RYR2 — something researchers had long suspected but never been able to prove as the cause.
Mutations of RYR2 cause a cardiac arrhythmic disorder that can result in seizures, exercise-related fainting spells and in the case of these Amish children, sudden death.
Lead scientist David Tester told CNN the gene mutation was a recessive disorder, meaning all the children likely had a common ancestor.
Mr Tester said the Amish could be more susceptible to inherited conditions because they inter-marry within the same US communities which is descended from a small pool of ancestors.
According to Michael Ackerman, director of the Windland Smith Rice Sudden Death Genomics Laboratory, the children that had died inherited a particular mutated RYR2 gene from each parent.
To prevent these deaths in Amish children Mr Ackerman said they were working on a medication which would prevent more fatalities.
Currently the only known solution for those who have inherited the mutation which makes them at risk of sudden death is an implantable cardioverter defibrillator — which is expensive and therefore out of reach for many families.
"We're going fast and furious to try to get this figured out for this Amish community," Mr Ackerman said.