Low HDL (usually thought of as <40mg/dL in men & <50mg/dL in women) is the bane of physicians. Regardless of LDL, the lower your HDL, the greater your risk of heart disease. However, we don't really have an easy way to increase HDL dramatically.
As physicians, we recommend strenuous intense exercise but we know how far that's gotten us. Wine makes a small increase but as we all know, too much of a good thing isn't. Niacin works but most won't tolerate the flushing & tingling side effects from doses high enough to make an impact. Fibrates can raise HDL some but requires a prescription. Of the statins used to lower LDL, only rosuvastatin raises HDL to some extent but doesn't have many outcomes studies yet. If you're diabetic, pioglitazone raises HDL while rosiglitazone tends to lower HDL. Recently, at the American Heart Association's annual meeting,
researchers announced their findings that Merck's experimental anacetrapib increased HDL substantially in a late phase clinical trial (by inhibiting cholesteryl ester transferase protein (CETP), if you must know). But it will probably be a while before this wonder drug hits the market, at which point we'll learn about its potential side effects (and financial cost).
So what do we do in the meantime? In a small, short 4 week
study published this month, authors asked 18 men & 25 women (average age 38-39 years old), all overweight or obese, to restrict both their caloric intake (down to 1800kcal/d for men & (1400kcal/d for women) and the resultant fraction of carbohydrates (on average from 55% down to 33% and from 53% down to 30%, respectively), commonly referred to as a "low carb" diet (goal <100g/d). They were instructed to maintain their current level of physical activity. In fact, the men were able to drop their average caloric intake down to 1307kcal/d while the women achieved 1243kcal/d.
As a result, men lost 4.7kg on average while women lost 2.4kg, resulting in significant decreases in body mass index. Furthermore, in the short term, both men & women decreased their waist circumference, body fat percentage, systolic blood pressure, total cholesterol, triglycerides, and insulin. Most importantly, men increased their HDL from 0.83mmol/L (32mg/dL) to 0.96mmol/L (37mg/dL). While this increase isn't enough to get these men out of harm's way (generally thought of >60mg/dL), it's certainly a step in the right direction without risk of drug side effects. Unfortunately, women demonstrated no significant increase in HDL.
It should be noted that this kind of eating wasn't easy to achieve. The researchers gave food products to minimize noncompliance since it was expensive to stay on this diet. In fact, only 7 of the 18 men were able to reach their goal of consuming <100g/d of carbohydrates.
What can we glean from this study? Well, it supports many other studies that have demonstrated an improvement in HDL by decreasing caloric intake and weight loss. However, it's not clear whether the increase in HDL was due to the caloric restriction, the decrease in carbohydrate consumption, or the weight loss. Let's not lose sight of the fact that this was a small, short study. But given the costs of most new drugs upon hitting the market and the relative lack of side effects (aside from the cost of food), it seems reasonable to recommend again that we eat less (carbs).
This site complies with the HONcode standard for trustworthy health information: 
