All people experience higher levels of endotoxins, which can lead to heart disease, after eating a meal high in saturated fat.
But a study to be presented at the Society for Endocrinology's annual meeting in Harrogate, Yorkshire, on Tuesday shows these levels peak at more than twice as high in people with type 2 diabetes.
Researchers warned that patients with type 2 diabetes should be wary of high fat, low carbohydrate diets that are promoted for weight loss.
Type 2 diabetics have raised background levels of endotoxin, bacterial fragments which enter the bloodstream from the gut and can cause inflammation and heart disease.
In the study, researchers led by Dr Alison Harte, research fellow at the University of Warwick, compared the effects of high-fat diet in 54 people. Fifteen were obese, 12 had impaired glucose tolerance, 18 had type 2 diabetes and 9 were non-obese controls.
Researchers monitored blood endotoxin levels for four hours, comparing baseline and post-prandial levels.
Although average levels of endotoxin increased for all participants, type 2 patients rose from 5.3 to 14.2EU/ml after four hours. This compared to a rise from 5.1 to 7.7EU/ml among the obese group.
Dr Harte said: 'High fat, low carbohydrate diets are often promoted to patients with type 2 diabetes as they have been suggested to aid weight loss and control blood sugar, but if confirmed in larger studies our data show that being healthy is not just about losing weight, as these particular diets could increase inflammation in some patients and with it the risk of heart disease.'