Even so, critics say the results show how hard it is to lose weight and keep it off.
"Early on, at eight weeks, they did fairly good jobs of following these four very different diets, but after 12 months, you could tell that these women had not followed the diets to the letter, and a lot of them had gone off them completely," Stanford University researcher Christopher Gardner, the lead author, told CBS Radio News.
"We actually weren't testing the diets as prescribed, we were testing the diets as people go out and buy the books and follow them on their own," he said.
Overweight women on the Atkins plan lost more weight over a year than those on the low-carb Zone diet. And they had slightly better blood pressure and cholesterol readings than those on the Zone; the very low-fat, high-carb Ornish diet, and a low-fat, high-carb diet similar to U.S. government guidelines.
Gardner said the study shows that Atkins may be more healthful than critics contend.
"This isn't necessarily a vindication of the Atkins diet, but I believe there's something inherent in the low-carbohydrate message that might be helpful for us to move in that direction," Gardner told CBS News' Tom Ryan. "I think the low-fat message that we tried for a long time back-fired on us. It was overly simplistic."
Proponents of other diets were critical of the findings.
The study "had a good concept and incredibly pathetic execution," said Zone diet creator Barry Sears.
"It's a lot easier to follow a diet that tells you to eat bacon and brie than to eat predominantly fruits and vegetables," said Dr. Dean Ornish, creator of the Ornish diet.
Atkins followers lost about 10 pounds on average at 12 months, versus 3.5 pounds for the Zone dieters.
Women on the Ornish diet lost almost 5 pounds on average and those on the national guidelines plan lost almost 6 pounds. Scientifically, those 12-month results weren't different enough from the Atkins weight loss to rule out the possibility the differences occurred by chance.
The dieters lost the most weight early on, including an average of 13 pounds for the Atkins group at six months — nearly double the closest competitor, the national guidelines diet. After that, most began regaining weight, a trend most noticeable in the Atkins women.
With an average starting weight of about 189 pounds, even losing 13 pounds meant many women remained overweight.
"There's not a ton of weight loss here," Gardner acknowledged. Atkins "isn't the solution for the obesity problem," he said.
The study involved 311 women about 40 years old on average and was designed to measure the effectiveness of using a diet book to lose weight. Women were randomly assigned to read one of four diet books. They attended weekly classes for eight weeks where diet questions were addressed, but then were mostly on their own for the next 10 months.
At the end, Atkins women had slightly higher levels of HDL cholesterol, the good kind, and slightly lower blood pressure than those on the other three diets. Gardner said differences in weight loss likely contributed to those results.
Ornish and other naysayers argued that the study doesn't answer a big question about the Atkins diet — whether consistently eating all that fatty food long-term leads to health problems.
The study appears in Wednesday's Journal of the American Medical Association.
The authors said it's uncertain whether the results would apply to men or older women since none were studied.
The study "shows that nothing works very well," said Yale University food policy researcher Kelly Brownell. His book promoting diet and lifestyle changes similar to national guidelines was used in the study.
"To me, it just screams out for the need to prevent obesity," Brownell said.
The results echo a Harvard study published last year involving thousands of women, which also suggested that a low-carb high-fat diet might be more heart-healthy than previously thought, although it relied on women's memories of what they had eaten over two decades.
Also, those who ate fat and carbs from vegetables rather than animal sources had lower heart disease risks in the Harvard study.
Dr. David Katz of the Yale Prevention Research Center and author of several weight control books, said the new study presents little new information and called it "much ado about nothing."
Nurse Jackie Eberstein, whose consulting company promotes the Atkins diet, said the results are not surprising. Protein makes people feel less hungry and fat helps them feel more full, which makes weight loss easier on Atkins, she said.
Study participant Viola Manges, who does administrative work at Stanford, was assigned to the Atkins group.
Manges, 41, said the diet taught her to make healthier food choices, like eating steamed vegetables instead of mashed potatoes, even if she didn't always follow it strictly.
"I realized I had a bunch of willpower I didn't even know I had," Manges said.
Manges lost roughly 23 pounds, slimming down to a size 6 by the study's end about a year ago. She has regained about 10 to 15 pounds, but said she still tries to follow some of the Atkins recommendations.
The study was funded by grants from the National Institutes of Health and from the Community Foundation of Southeastern Michigan.