As with many foods and food ingredients, there is argument over whether or not High Fructose Corn Syrup (HFCS) is safe to use. Some of this controversy stems from the origin of its introduction into our food supply as well as the simple argument of whether or not it is a natural sugar. In order to understand why there is such controversy over HFCS, it is important to know and understand the history that sugar has played in our society.
Interestingly, sugar has played a huge role in American history dating back to the early years of slavery as well as being one of the first items to hold a national tax. During most of American history, there have been tariffs paid on imported sugar. A debated topic through most of the 18th, 19th and even 20th century was whether or not America should be an independent nation, free of reliance on other nations, or if America should have open trade with other nations. This concept is known as Protectionism and was one of the leading causes of the Civil War.
One of the protectionist issues debated involved sugar, indirectly. The Protectionists, who wanted an independent America, believed that if they added a tariff to imports such as sugar it would discourage American companies and consumers from buying imports, and instead, would buy from American farmers. This theory worked until the early part of the 20th century when sugar became so cheap overseas that even with tariffs, imported sugar became cheaper to buy than American sugar.
This issue was dealt with numerous times through Farm Bills and Sugar Acts in Congress; however the tariff came to an end in the Sugar Act of 1934. It was replaced with a new system (in order to deal with the new economic issues) that was changed many times throughout the 1930’s into the 1970’s. 
It was in the late 1960’s and early 1970’s that HFCS was first introduced to the marketplace. Under the Nixon Administration, Secretary of Agriculture Earl Butz, had re-introduced a system of farm subsidization for farmers in an effort to deal with the economic situation that farm products needed to be cheap for consumers, yet farmers needed to make enough profit to survive. Part of this legislation was to replace sugar with HFCS. The reason was that it would create two beneficial aspects; it would help the corn farmers earn a profit and it would create cheaper products for consumers. The government also planned to use the corn products to launch a program for using ethanol in vehicles rather than gasoline. The two products complemented one another, helping the farm industry as well as keeping more money in the U.S. As a result of these decisions, HFCS is now the primary sugar found in most “sugar-added” products such as cereals, breads, juices, soda, sweetened beverages, jams, and condiments.
Proponents of using HFCS claim that it is made from fructose and glucose and comes from a natural food product, corn, and is therefore a natural sugar. There have also been numerous studies performed, funded by companies such as the American Beverage Association, Archer Daniels and PepsiCo, that have results claiming there is no biochemical differences in the body between HFCS and table sugar. 
However, opponents claim that it is a highly processed sugar, thus not a natural sugar. They believe there is evidence demonstrating that it is a cause of obesity and metabolic disruption and want to see it removed from foods and replaced with natural sugar. There are many books and articles written by health food advocates protesting the use of HFCS. Whether or not there is any validity to their protests is yet to be determined, however the belief that HFCS is bad for health is a popular theory.
Knowing the real answer is difficult. There have been studies demonstrating that fructose, and not high fructose corn syrup, may effect obesity as well as regulatory hormones. However, this is ambiguous at best as fructose is typically found as part of larger sugar molecules in many natural food sources.
While more studies (preferably not funded by any company or association affiliated with HFCS) need to be done to show any true correlation between HFCS and obesity or metabolic disruption, it is a good idea to reduce your sugar intake, period, whether it is from HFCS or table sugar.
 The American Sugarbeet Growers Association. ”History of Sugar Programs”. http://www.americansugarbeet.org/ 4 Dec 2007.
 Nestle, Marion. Food Politics. Berkeley, CA: University of California Press, 2002.
 K.J. Melanson et al. “Effects of high-fructose corn syrup and sucrose consumption on circulating glucose, insulin, leptin, and ghrelin and on appetite in normal-weight women”. Nutrition 23 (2007) 103-112.
 MW Empie et al. “Lack of findings for the association between obesity risk and usual sugar-sweetened beverage consumption in adults”. Food and Chemical Toxicology, Volume 45, Issue 8, August 2007, Pgs. 1523-1535.
 RA Forshee et al. “A critical examination of the evidence relating high fructose corn syrup and weight gain”. Food Science and Nutrition, 47:561-582 (2007).