Agave nectar has a low-glycemic index for one reason only: it's largely made of fructose, which although it has a low-glycemic index, is probably the single most damaging form of sugar when used as a sweetener. With the exception of pure liquid fructose, agave nectar has the highest fructose content of any commercial sweetener.
Fructose -- the sugar found naturally in fruit -- is perfectly fine when you get it from whole foods like apples (about 7 percent fructose) -- it comes with a host of vitamins, antioxidants and fiber. But when it's commercially extracted from fruit, concentrated and made into a sweetener, it exacts a considerable metabolic price. Fructose has also been linked to non-alcoholic, fatty-liver disease. Rats that were given high fructose diets developed a number of undesirable metabolic abnormalities including elevated triglycerides, weight gain and extra abdominal fat.