The family immediately agreed and the operation took place at Great Ormond Street Hospital in March 2010.
Since then Ciaran, from County Down in Northern Ireland, has grown almost four-and-a-half inches (11cm) and he has returned to school. He has also been able to develop his musical interest as a drummer. A medical update is published in The Lancet today.
His family has declined to be interviewed, but at the time of the operation his mother Colleen said she and her husband Paul had got our boy back.
The procedure involved taking a windpipe from a 30-year-old Italian woman who had died and stripping it of living cells down to the inert collagen scaffold.
Four weeks later, Ciarans windpipe was removed. Sections of its lining were taken off and kept and the rest discarded. Bone marrow from Ciaran was harvested and the stem cells isolated.
The same day, the donor windpipe was inserted into Ciarans neck and his stem cells sprayed on to it.
Tiny sections of lining from his original windpipe were patched on to the replacement. These prompted the stem cells to turn into the right kind of tissue and kick-started growth of the windpipe lining.
Finally, the graft was injected with proteins to stimulate cell growth and differentiation, called cytokines.
The operation was the first attempt to grow stem cells in place in the body of a child, rather than growing an organ in a laboratory bioreactor.
It came only two years after the first windpipe replacement using stem cells in an adult, although in that case, carried out in Barcelona, the organ was grown in the lab.
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Pioneering windpipe boy growing into healthy teenager