This paper presents a rapid HPLC method for the separation of isomaltulose (also known as Palatinose) from other common edible carbohydrates such as sucrose, glucose, and maltodextrins, which are commonly present in food and dietary supplements. This method was applied to determine isomaltulose in selected food supplements for special diets and athletic performance. Due to the selectivity of the separation system, this method can also be used for rapid profiling analysis of mono-, di-, and oligosaccharides in food.