Children born by Caesarean section have a 20% higher risk of developing type 1 diabetes than those born naturally, says a report in PubMed journal.
This form of diabetes, which can start in early childhood, is on the rise in Europe and scientists are unsure why.
Queen's University Belfast examined 20 past studies, suggesting contact with hospital bacteria rather than maternal bacteria in delivery may be to blame.
The normal risk of a baby developing type 1 diabetes is three in 1,000.
"Not all women have the choice of whether to have a Caesarean or not, but those who do may wish to take this risk into consideration before choosing to give birth this way"
It is a potentially dangerous condition which, even if properly controlled, can mean a lifetime of blood tests and insulin injections.
There are an estimated 250,000 people in the UK with this type of diabetes, compared with more than two million with type 2 diabetes, which develops later in life.
The 20% rise could not be explained by other factors such as birth weight, breastfeeding, the age of the mother, or conditions such as gestational diabetes during pregnancy.
In the UK, an average of 24% of deliveries are by Caesarean section, well above the 15% recommended by the World Health Organisation.
While many are needed to protect mother or child during delivery, research suggests doctors may be too quick to recommend Caesareans in some cases, and that some mothers opt for them for non-medical reasons.
Environmental factors
Dr Chris Cardwell, from Queen's University Belfast, said: "This study shows a consistent 20% increase in the risk of diabetes.
"It is important to stress that the reason for this is still not understood, although it is possible that the Caesarean section itself is responsible, perhaps because babies born via that method are first exposed to bacteria originating from the hospital environment rather than to maternal bacteria.
"Type 1 diabetes in childhood has become more prevalent across Europe recently, and the rate of this increase suggests that environmental factors are the cause.
"However, despite much investigation, these actual factors remain largely unknown."
Dr Iain Frame, from Diabetes UK, said that genetics and childhood infections were known to play some role in type 1 diabetes, but more research was needed into the possible Caesarean link.
"The findings of this study indicate that the way a baby is delivered could affect how likely it is to develop this condition later in life.
"Not all women have the choice of whether to have a Caesarean or not, but those who do may wish to take this risk into consideration before choosing to give birth this way."
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