Updated February 15, 2014.
The Results
The participants following the Atkins diet lost an average of 14.7 pounds compared with 5.8 pounds in the conventional group at 3 months; 15.2 pounds versus 6.9 pounds at 6 months; and 9.5 pounds versus 5.4 pounds at 12 months.
At 1 year, Atkins participants had greater increases in HDL cholesterol (18% vs. 3%) and greater reductions in triglycerides (-28% vs. 1%) than did those following a conventional diet.

Neither group showed changes in LDL (bad) cholesterol at 1 year. Dr. Foster stated:

• "...Widely recommend low carbohydrate approaches may be premature, but our initial findings suggest that such diets may not have the adverse effects that were anticipated."
  "The real issue is whether low carbohydrate approaches help patients maintain their weight loss better than conventional approaches. It will also be important to determine whether the effects of the diet on cholesterol are the same during weight maintenance as they are they are during weight loss," he said.
  

Second Study Shows Similar Results
Another group of Penn faculty working at Philadelphia VA Medical Center reported similar findings in the New England Journal of Medicine.

In their 6-month study, Frederick Samaha, MD, and colleagues, found that a low-carbohydrate diet was associated with greater weight losses, reductions in triglycerides, and improvements in insulin sensitivity compared to low-calorie, high-carbohydrate diet.