Advocacy groups have been pushing to limit unhealthy snacks and the ads promoting them for years.
"Given the high rates of childhood obesity and children's poor diets, it doesn't make sense to advertise and market unhealthy food to children at all, much less in schools," said Margo Wootan, Center for Science in the Public Interest's nutrition policy director.
CSPI says that in 2012, 70 percent of elementary and middle school students and 90 percent of high school students attended schools that allowed food marketing, most of it for unhealthy food.
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The Federal Trade Commission says the heaviest marketers are candy and snack food manufacturers, beverage companies and fast-food restaurants, which make use of posters and scoreboards.
They also give students coupons, for instance offering pizza as a prize for students who read a certain number of books, and they place advertisements in school television programs and other educational materials.
California banned sodas and junk food from public schools in 2005 and Connecticut did so in 2006, but most states don't have policies.
"Our priority is supporting the health of kids and they shouldn't be targeted for the marketing of junk foods and drinks," said Sam Kass, executive director of Let's Move.
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Ads for junk foods such as candy bars, potato chips and other treats that don't conform to the U.S. Department of Agriculture's Smart Snacks in School guidelines would be banned under the proposed rules. Those recent USDA guidelines limit calories, sugar, and fat content in food sold to students at 100,000 schools. Concessions sold at after-school sports games would be exempt.
As much as 90 percent of marketing for unhealthy foods in schools is related to beverages, and companies have already started to adjust. Under the proposal, beverage companies could market their branded lines of bottled water, but not sugary soft drinks.
"The new standards ensure that schools remain a safe place where kids can learn and where the school environment promotes healthy choices," U.S. Agriculture Secretary Tom Vilsack said in a statement, adding that they want to "make the healthy choice, the easy choice for America's young people."
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The beverage industry — led by companies Coca-Cola, Dr Pepper Snapple Group and PepsiCo — is on board with the move. In a statement, American Beverage Association President and CEO Susan Neely said that aligning signage with the healthier drinks that will be offered in schools is the "logical next step."
"Mrs. Obama's efforts to continue to strengthen school wellness make sense for the well-being of our schoolchildren," Neely said.
—By NBC News's Maggie Fox. The Associated Press contributed to this article.