Last school year, lunchrooms across the nation got a dietary makeover. New rules banished 2 percent and whole milk from the National School Lunch Program.   

This month, Illinois’ Women Infant and Children feeding program followed suit by now offering skim and 1 percent almost exclusively.

“This was a decision by the United States’ Department of Agriculture, who funds our program,” says Stephanie Bess program director for Illinois WIC. “It’s designed to align our food packages with the messages that we provide to our participants. Since 1995, the dietary guidelines for Americans have recommended low-fat milk.”

But critics say, 1995 was a long time ago, and that these guidelines have almost no scientific evidence to back them up.

Dr. David Ludwig directs the New Balance Foundation Obesity Prevention Center at Boston Children’s Hospital. He wants to see better science behind the program decisions.

“It seems to make sense that if we just got rid of the saturated fat in milk there could be health benefits and there would be weight loss and lower cardiovascular disease risk factors,” Ludwig says. “Unfortunately, there is virtually no evidence that reducing fat in milk will have any health benefits at all.”

Last year, Ludwig wrote an editorial with Harvard’s Public Health chief Walter Willett warning officials against low-fat school milk. They represent a growing group of scientists and doctors who say the low-fat dietary guidelines run counter to public health.

USDA representatives declined to be interviewed for this story, but offered a written statement saying the recommendations came from “experts in health, nutrition, school food service, and economics.”

Bess of Illinois WIC tried to explain the agency’s rationale.

“As a registered dietician, I am looking at the diet as a whole, which is what we do at WIC,” she says. “Milk is one component of that and this is more than a calorie issue. This is about saturated fat.”

Still, as many point out, analyses from Harvard and Cambridge University researchers now suggest that saturated fat is not to blame for heart disease. Instead, it’s carbohydrates that appear to be the villain. In fact, new government research suggests a high-fat, low-carb diet is much more effective for weight loss than a low-fat diet.

Last year, researchers at the University of Virginia School of Medicine looked at 10,700 children and found that those who drank skim and one percent milk were much more likely to be overweight and obese than those who drank 2 percent or whole milk. In fact, children who started at normal weight and drank low-fat milks were 57 percent more likely to become overweight than those who drank higher fat milks.

Nina Tiecholz wrote “The Big Fat Surprise.” It charts the rise of obesity in the US as citizens followed government advice to cut fat, especially saturated fat, in their diet. She said she was heartbroken by the news on WIC.

“To me it’s devastating because without the fat in milk you cannot digest the fat soluble vitamins A and D,” she says. “They are essential and without them you can’t absorb the minerals in milk. So milk is much less nutritious when you take out the fat.”

Ludwig notes that these low-fat milks lose flavor along with those calories.

“And there’s the tendency to replace those calories with sugar like chocolate milk and that trade off is not good for children’s health,” he says.

Indeed, today skim chocolate milk is the No. 1 beverage served in the federal lunch program.  

“Milk that’s high in sugar and low in fat is the worst possible kind of beverage you could be serving them,” Teicholz says, noting the lower nutrition absorption and adding, “Sugar triggers the release of insulin, which is the king of all hormones for making you fat.”

USDA officials, however, disagree. They say the added sugar is worth it if it gets kids to drink the milk.

“Studies have shown consistently over the country that if you take out that option [for chocolate milk] even though it’s non-fat, the milk consumption goes down,” says USDA undersecretary Concannon.

And while the American Heart Association doesn’t support sugary school milk, it does support the the switch to low-fat white milk in WIC. Still, the heart association’s Mark Peysakhovich says they’re also open to considering any new data the move might bring.  

“This is a once in a lifetime opportunity to study the effects of low fat milk on this population,” he says. “And that’s part of what’s so exciting about this move.”

To find out if the USDA will also considered the new data, you won’t have to wait long. New dietary guidelines are due out in 2015.

Monica Eng is a WBEZ food and health reporter, and co-host of the Chewing The Fat podcast. Follow her at @monicaeng or write to her at meng@wbez.org