These mutations may result in one of the twins having autism or other developmental disorders, while the other does not.
The average number of differences between the genomes of monozygotic twins has never before been known.
The types of mutations leading to these differences were also not known nor when in the early stages of embryonic development they occur.
But a team, led by Hákon Jónsson of the University of Copenhagen, now believe they have the answer. They sequenced the genomes of 387 pairs of identical twins and their parents, spouses and children to track mutation divergence.
The authors found that twins differ by 5.2 early developmental mutations, on average.
The study also found that in approximately 15 per cent of identical twin pairs, one twin carries a high number of these mutations that the other twin does not have.
The authors write that differing traits between monozygotic twins has "generally been attributed to the environment".
"This assumes that the contribution of mutations that separate monozygotic twins is negligible; however, for some diseases such as autism and other developmental disorders, a substantial component is due to de novo mutations."
Identical twins come from a single zygote formed by one sperm fertilising one egg.
Fraternal or dizygotic twins are formed by two eggs that are fertilised by two sperm and produce two genetically unique children.
The study concluded that the role of genetic factors in shaping such phenotypic differences between identical twins has been underestimated.
"Our results indicate that allocations of cells during development shapes genomic differences between monozygotic twins," they said.
