They found that people who ate these foods the most were also more likely to be overweight or obese and to have unhealthy levels of cholesterol and blood sugar.
And the researchers, led by Karen R. Siegel, of the Centers for Disease Control and Prevention, tie their findings directly to U.S. subsidies.
"The U.S. Department of Agriculture and U.S. Department of Health and Human Services Dietary Guidelines for Americans emphasize consumption of fruits, vegetables, whole grains, protein and moderate amounts of dairy, while recommending limited consumption of saturated fats, sugars, salt and refined grains," Siegel's team writes in the Journal of the American Medical Association's JAMA Internal Medicine.
"At the same time, current federal agricultural subsidies focus on financing the production of corn, soybeans, wheat, rice, sorghum, dairy and livestock, the latter of which are in part via subsidies on feed grains."
The policies have been controversial for years, with health experts saying the U.S. government should drop subsidies on beef, dairy and other products and instead help farmers raise cheaper fruits and vegetables.
But USDA and other experts argue that it's not so simple to tie subsidies to American eating habits and say the beef, dairy and grain industries are important for the U.S. economy.
To answer the question, Siegel's team looked at just over 10,000 people who took part in a federal survey that included a list of what they had eaten the day before.
They found that on average, 56 percent of the calories people remembered having eaten came from the major subsidized foods.
And those who ate the most of these foods were 37 percent more likely to be obese and 41 percent more likely to have too much belly fat. They were 14 percent more likely to have high cholesterol and 21 percent more likely to have unhealthy blood sugar levels.
"The present finding that higher subsidy scores are associated with adverse cardiometabolic risk highlights the effect that agricultural subsidies may be having on health disparities in the United States, in part due to the lower cost per calorie of unhealthier food and the higher cost per calorie of healthier food," they wrote.
"Although eating fewer subsidized foods will not eradicate obesity, our results suggest that individuals whose diets consist of a lower proportion of subsidized foods have a lower probability of being obese."
But Raj Patel of the University of Texas at Austin says it's no quite so simple.
While cheap food is one big cause of America's epidemics of obesity, heart disease and diabetes, junk foods that are not subsidized are a large part of the equation, he wrote in a commentary.
"Furthermore, among a range of agricultural products, farmers receive the greatest share of the retail price in beef and milk at 50 percent compared with only 7 percent for processed food, such as bread," Patel wrote.
"So, while processed food prices may be low, commodity subsidies are not the primary cause."
Doctors need to do more to help Americans drop their addiction to cheap, unhealthful food, Patel said.
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