Scientists from the Murdoch Childrens Research Institute (MCRI) in Melbourne studied the DNA of a group of identical and non-identical twins, using the placenta, umbilical cords and cord blood collected at birth.
They found that although identical twins share the same DNA sequence the chemical markers that switch genes on and off were different.
This process, known as epigenetics, can affect gene activity and influences normal development and conditions such as diabetes and heart disease.
"It's been known for some time that identical twins - twins with the same DNA sequences - can look different, can behave different and can have different health conditions," MCRI researcher Jeff Craig said.
"In rare cases this can be down to genetic differences but it can't explain everything.
"The differences that we think are most important are the epigenetic differences."
Dr Craig said the study showed the environment in the womb played a critical role in setting up this epigenetic profile.
"This must be due to events that happened to one twin and not the other whilst in the womb," he said.
Dr Craig said although twins share a womb, their nutritional supply line from either the placenta or the umbilical cord could be different for each foetus and this would effect the epigenetic profile.
The research team found gene changes associated with low birth weight were involved in metabolism and heart disease.
Co-leader of the study Dr Richard Saffery of the MCRI said the breakthrough could eventually enable doctors to identify and track disease early in life, or introduce diet or environmental changes to reduce the risk.
Dr Craig said the discovery showed that there were some elements of fetal development which were out of mothers' control.
"A pregnant mother can alter her diet and lifestyle...but our study is showing that there are factors beyond that, that are almost beyond our control," he said.
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