The scientists from the University of Texas say this applies to people with even small pot bellies.
In a study involving 2,700 men and women between the ages of 18 and 65 the participants had a total of three medical visits each.
Each visit included an in-home health survey, blood and urine collection, and a detailed clinical exam including abdominal magnetic resonance imaging and coronary artery calcium scans to determine if they had atherosclerosis; atherosclerosisis the narrowing of arteries and is the earliest sign of impending heart disease.
The researchers compared these measurements with that of the body weight of the subjects.
They found that even a small increase in Waist to Hip Ratio (WHR) increased the risk of heart disease even if the person's body weight was normal.
Those with high WHR were most likely to have calcium deposits in their arteries indicating atherosclerosis compared to those with low WHR.
The researchers believe that fat which accumulates around the waist appears to be more biologically active as it secretes inflammatory proteins that contribute to atherosclerotic plaque build-up; but fat around the hips does not appear to increase risk for cardiovascular disease at all.
Lead researcher Professor James de Lemos says the key message for people is to prevent accumulation of central fat early on in their lives by developing lifelong dietary and exercise habits that prevent the development of the 'pot belly'.
The team found the risk of heart disease in people with high WHR remained even when factors such as age, blood pressure and diabetes were taken into consideration.
The study indicates that a woman having a waist size of 81cm and a man having waist size of 94cm face a high risk of developing heart disease.
The research was part of the Dallas Heart Study, a multiethnic, population-based study of more than 6,000 patients designed to examine cardiovascular disease.
The study aims to gather information to help improve the diagnosis, prevention and treatment of heart disease and is published in the Journal of the American College of Cardiology.
The researchers suggest that the 'pleasure chemicals' released by the mother when eating junk foods might have an effect on the developing brain of the foetus.
Professor Neil Stickland, who led the research, says the research shows that while the government is trying to encourage healthier eating habits in schools, the process needs to begin during the foetal and suckling stages of life.
Professor Stickland says it is not just about genetics as the study shows a direct link to what the mothers eat and how it affects their children.
Experts warn against making women feel guilty about eating some unhealthy snacks during pregnancy and say that is when a balanced diet is important.
They also say data in human studies are needed to add support to the findings.
According to the World Health Organisation around 400 million people are now obese, including 20 million children under the age of five and obesity is a major issue worldwide as it raises the risk of diseases such as type 2 diabetes and heart problems.
The research was funded by the Wellcome Trust and is published in the British Journal of Nutrition.