Examination of 24 victims of unexplained cot deaths showed that two-thirds had under-developed kidneys.
The abnormality, which occurred in the womb, would have left the babies vulnerable to dehydration, or a build-up of toxins, in the first six months of life, either of which can prove fatal.
This could explain factors linked with cot death, such as infection, over-wrapping or sleeping position. Such problems would probably be shaken off by a healthy baby but could kill a vulnerable one.
Dick van Velzen, professor of foetal and infant pathology and leader of the team at Liverpool University, described the findings as 'extremely significant'.
The scientists believe impaired growth in the womb of other vital organs, especially the lungs and brain, may also be connected with cot deaths.
They think there is a common link, a condition called Uterine Growth Retardation (UGR), which results in some babies being born smaller than they ought to be. Even a 'normal-sized' infant can fall into this category, if it is smaller than it would have been without UGR.
The breakthrough was achieved using microscope technology developed by Dr Vyvyan Howard, a senior lecturer in Professor van Velzen's department.
For the first time this allowed an accurate count to be made of the number of nephrons, or filter units, in the kidney. Healthy babies should have more than a million nephrons in each kidney, but the cot-death victims examined had far fewer - in some cases only 350,000.
In 1991, 1,134 babies under one year old were cot-death victims in the United Kingdom.