It's been the case that any weight loss (even small amounts, in this case ~3% across diets) gives rise to an improved cardiovascular disease (CVD) profile. Gardner, et al., looked at this. They "examined the independent effect of diet group on secondary outcomes [HDL, triglycerides, BP, etc.] after adjusting for 12-month changes in weight."
Women in the Atkins group had better HDL, triglyceride, and blood pressure measurements independent of weight loss. It appears that the protein, carbohydrate, and fat proportions of their diet had a beneficial effect on their blood values whether they lost weight or not. (Although weight loss still improved these figures.)
Here are some CVD risk factor changes in these women after a year. Keep in mind that variation was so great, only a few of these changes reached significance, mostly in favor of Atkins.
Click for larger.
* From the study: "Although a higher LDL concentration would appear to be an adverse effect, this may not be the case. ... The triglyceride-lowering effect of a low-carbohydrate diet leads to an increase in LDL particle size, which is known to decrease LDL atherogenicity."
This isn't the first study to show that a low-carb diet results in increased HDL (the "good" cholesterol) and decreased triglycerides. But when you lower carbs, you automatically increase fat and protein. And isn't fat the felon? Maybe not.
Perhaps more generous amounts of fat in the diet (recall fat consumption in Atkins eaters relative to the others, last graph in post) might not be as harmful as we are led to believe, if that fat, along with protein, is replacing, not adding to, carbohydrate calories. Even better, if it's replacing highly processed (high glycemic index) carbohydrate calories. (The type of fat we should eat? This study did not elucidate. Although Atkins women were eating about 7g more saturated fat than the other groups.)
There was an emphasis on reducing intake of simple/processed carbohydrates and sugars in all 4 diets. If women abided this, it remains that reducing overall amount of carbohydrate, not just switching to complex carbs (low GI), may benefit CVD outcome.