A new study comparing the Atkins diet, a Mediterranean diet and a low-fat diet published on July 17 inThe New England Journal of Medicine (NEJM), is likely to inspire headlines saying that the Atkins diet is better for your waistline and your health than a low-fat diet.

However, as a lead investigator on numerous peer-reviewed studies of low-fat diets, and the author of several books about the benefits of healthy low-fat lifestyles, I believe this study is extremely flawed. Here's why:

The NEJM study, which was funded in part by the Atkins Foundation, reported that participants who ate a low-carb (Atkins) or Mediterranean diet (restricted calorie, moderate fat intake) for two years lost more weight, and saw more of an improvement in their glucose and cholesterol levels, than those who were on a low-fat, restricted calorie diet. However, participants in the study who were on the "low-fat" diet decreased their total fat intake from 31.4 percent to 30.0 percent, hardly at all.

I'm also very skeptical of the quality of data in this study. For example, the investigators reported that those on the "low-fat" diet consumed 200 fewer calories per day—or 10,000 fewer calories per year—than those on the Mediterranean diet, yet people lost more weight on the Mediterranean diet. That's physiologically impossible.

In addition, in the "Atkins diet" that was tested, "the participants were counseled to choose vegetarian sources of fat and protein and to avoid trans fat." A vegetarian Atkins diet?  Most people associate an Atkins diet with bacon, butter and brie, not a plant-based diet like the one I recommend.

Then there's the question of what constitutes a "low-fat" diet. The one used in the NEJM study was not very low in fat. It was based on the American Heart Association (AHA) guidelines, which I have long criticized as not being enough of a change in diet to show much benefit. In earlier studies, as in this one, the AHA diet did not cause much of a reduction in either blood cholesterol levels, weight or blood sugar, so it's not surprising that the new NEJM study reported that the Atkins and Mediterranean diets were more successful at reducing these levels. In the Womens Health Initiative study, the AHA diet didn't do much to prevent heart disease, colon cancer or breast cancer, either.

My colleagues and I at the nonprofit Preventive Medicine Research Institute and the University of California, San Francisco, have studied for more than three decades the effects of diets much lower in fat (10 percent) than the one used in NEJM study as well as lower in refined carbohydrates and higher in fruits, vegetables, whole grains, legumes and soy products.

We reported in a randomized, controlled clinical trial published in the Journal of the American Medical Association a 24-pound weight loss after one year and 13-pound average weight loss after five years in a group of men and women, much more than the 9.7 to 10.3 pounds lost in the new NEJM study.  These findings were replicated in larger demonstration projects as well.