Babies born by Caesarean section may have a greater risk of suffering food allergies and diarrhoea during their first 12 months, research suggests.
There are health concerns about Caesareans
A team at Munich's Ludwig-Maximilians University studied 865 babies all fed on breast milk until four months.
They found C-section babies were more likely to have diarrhoea in their first year, and were twice as likely to be allergic to cows' milk and other food.
The research is published in Archives of Disease in Childhood.
All the babies in the study were born into families with a history of allergies.
They were monitored at one, four, eight and 12 months of age.
Blood samples were also taken after 12 months to check for signs of an allergic response to foods, including eggs, cows' milk proteins, and soy protein.
And during the first six months, their mothers completed weekly diaries on their children's health and feeding.
In all, 147 of the 865 babies had been born by C-section, a rate of 17%.
The researchers say previous work has suggested that gut bacteria play a key role in the development of the immune system.
They believe that C-section alters or delays the "normal" bacterial colonisation of the baby's gut.
It may be that vaginally delivered babies pick up bacteria from the mother's vagina, intestine and anal area, whereas babies born by C-section merely acquire bacteria from the hospital environment.
Dr Basky Thilaganathan, consultant in foetal medicine at St George's, told BBC News Online: "Caesarean section is not a physiological way of being born, and so it is not surprising that this method of delivery might lead to a slight difference in the way the immune system develops."
However, Dr Thilaganathan said there were a number of flaws in the study which raised questions about the veracity of its findings.
A quarter of the babies born by C-section were born two to three weeks before full term, he said, and therefore subsequent problems might simply be due to the relatively immature state of the immune system at birth.
In addition, a higher number of the C-section babies were first children than those born by vaginal delivery.
It was well known, said Dr Thilaganathan, that first-time parents were more likely to report even minor symptoms than those who had previously had other children.
Dr Thilaganathan also said that many of C-sections were done during labour, casting doubt on the theory that these babies were not exposed to their mother's bacteria.
Finally, he said the study had not set out to show a link between C-section and allergy, and that this might simply have been thrown up by chance as a result of an intensive statistical analysis of the data.