There have not been any studies that show that low-carb diets are either harmful or safe in the long run. Plenty of short-term studies exist that show that although it's possible to lose more weight after six months on a low-carb diet, there was no difference between a low-carb diet and a low-fat diet after a year of dieting.
The National Institutes of Health is in the midst of a 5-year study of 360 patients that compares low-calorie and low-carbohydrate diets. Effects of long-term low-carb, high-fat eating on kidney function will also be examined during that study. There are some side-effects associated with low-carb diets, including constipation, diarrhea, headaches, bad breath, muscle cramps and weakness.
"Two Studies Weigh In on Low-Carb Diets." American College of Physicians. May 2004. ACP. 16 Jul 2007