Background: Saturated FATty acids (SFA) and trans isomer of unsaturated FATty acids (TFA) are shown to be associated with endothelial damage. Until now there are different reports about the severity of their damage on the endothelium. The aim of this study was to compare the effects of SFA and TFA on endothelial function through evaluating the flow mediated vasodilatation and serum proinflamatory markers.Methods: In a prospective clinical trial, which was conducted in January 2008, 17 healthy volunteers were recruited in the study. The study was done in two days. In the first day the participants have eaten boiled bens with 25 grams of hydrogenated vegetable oil added. Flow Mediated vasodilatation (FMD), C-reactive protein, E-selectin, soluble Intercellular adhesion molecule (sICAM-1), soluble vascular cellular adhesion molecule (sVCAM-1), and interleukine 6 were checked before and 4 hour after test meal. After 7 days, second day of the study, the participants were took part in the study the same as the first day, but they have eaten boiled been with 25 grams animal oil added. Samples of animal oil and hydrogenated vegetable oil were analyzed for its FATty acid composition using gas chromatography.Fidings: There was no significant difference between the levels of fasting serum markers and flow mediated vasodilatation (FMD) in two days of the study. FMD was decreased after eating both animal oil (rich in saturated FATty acids) and hydrogenated vegetable oil (rich in Trans isomer of unsaturated FATty acids). However, there were not significant differences between the serum markers and FMD after 4 hours of eating test meals in both days of the study.Conclusion: Saturated FATty acids and Trans isomer of unsaturated FATty acids may equally harmful to the endothelium.