A team from the University of Edinburgh and Queen Margaret University analysed the health records of children from South East Scotland aged under 16 years who were newly diagnosed with the condition between 1990 and 2009.
The team - based at Royal Hospital for Sick Children in Edinburgh - found that the rate of children being newly diagnosed with Coeliac disease rose from 1.7 in every 100,000 children in 1990-1994 to 11.8 per 100,000 children in 2005-2009.
Coeliac disease only affects those who carry the gene for the condition. It is triggered by what doctors call an 'infective hit' - often a viral infection such as gastroenteritis - causing the immune system to attack the lining of the intestines.
Such damage can cause symptoms such as weight loss, abdominal pain and stunted growth, although doctors say that in many older children and adults, recurrent abdominal pain may be the only symptom.
At its most serious, Coeliac disease may cause children to become malnourished. Experts say that the driving force of the condition is a reaction to foods that contain gluten - including wheat, barley and rye cereals.
The Edinburgh team adds that while it does not yet know what is responsible for the rise in Coeliac disease cases, there are a number of possible explanations.
Factors could include changing patterns of childhood infection because of on-going improvements in healthcare as well as an increase in the incidence of related autoimmune conditions - including Coeliac disease and Type I diabetes.
Researchers say that while the trend could reflect a growth in awareness of the condition, they have also seen a rise in the number of classical - more severe cases - which are more likely to affect younger children.
Dr Peter Gillett, of the University of Edinburgh's Department of Child Life and Health and the Royal Hospital for Sick Children, Edinburgh, who led the study, said: "This study confirms a trend we have seen on a daily basis in our local area of Lothian, Fife and Borders. It also confirms the need to look further at factors influencing why we are seeing more patients with Coeliac disease- it is not only because people are more aware of the disease nor is it thanks to our improved tests.
"Although the number of patients that we are diagnosing with the disease is increasing, it is well short of the number of cases out there, as screening the general population would pick up around one in 100 people.
"The increase in pick-up has implications for families and the support from healthcare they require to maintain a strict lifelong gluten free lifestyle once the diagnosis is made."