The best supplement I know of to increase HDL is niacin.   Niacin (nicotinic acid), also known as Vitamin B3, is important for the normal function of many bodily processes. Like other B vitamins, it is water-soluble and plays a role in turning food into energy, as well as in the metabolism of fats and carbohydrates.  Niacin can also act as an antioxidant within cells, which means it can destroy cell-damaging free radicals. In conjunction with riboflavin and pyridoxine, it helps to keep the skin, intestinal tract and nervous system functioning smoothly.

General use

The recommended daily allowance (RDA) of niacin for infants under six months is 5 mg. Babies from six months to one year of age require 6 mg. Children need 9 mg at one to three years of age, 12 mg at four to six years, and 13 mg at seven to 10 years. Women need 15 mg from 11-50 years, and 13 mg thereafter. Somewhat more is required for pregnancy (17 mg) and lactation (20 mg). Men require 17 mg from 11-14 years of age, 20 mg from 15-18 years, 19 mg from 19-50 years, and 15 mg at 51 years and older.  Niacin displays potent abilities to lower LDL (bad) cholesterol and triglyceride levels and elevate HDL (good) cholesterol levels. More
importantly, niacin has also been shown to promote the regression of hardened arteries and to decrease the incidence of heart disease and its associated deaths.

Niacin, in the form of nicotinic acid, can be taken in very large doses to decrease cholesterol and reduce the risk of heart attack. The amount required is between 2 and 3 g. This is not a therapy that should be undertaken without professional medical advice and supervision. Certain conditions preclude the use of high doses of niacin. These include gout, diabetes, peptic ulcer, liver or kidney disease, and high blood pressure requiring medication. Even in the absence of these conditions, a patient on high doses of niacin should be closely monitored to be sure the therapy is both effective and without complications. The immediate release niacin is hard to tolerate because of a frequent side effect, which is extreme flushing of the face and neck. It is harmless, but can be unpleasant.  There are two niacin compounds marketed as "no-flush".  One is niacinamide, which one article claim doesn't work. The other
no-flush niacin is inositol hexanicotinate, which worked great for me.  I took four of the 500 mg Source Naturals inositol hexanicotinate per day and my HDL went from 34 to 67.  I read somewhere that an extremely high carbohydrate diet can decrease HDL but I can't find the article.  Part of my HDL increase may have been from increasing fat in my diet.   I started snacking with a slice of whole wheat bread with the non-hydrogenated peanut butter and strawberry jam sweetened only with fruit juices on top.  I tried the prescription Niaspan and that had significant flush also.  I didn't experience any side effects from the inositol hexanicotinate. "Slow release" niacin also causes less flushing, but should not be taken as there is higher risk of liver inflammation.

In his article, Flushing Away Heart Disease , Anthony Hamada. MS, indicated that a recent study suggests that niacin (average dose of 2.1 grams per day) can produce favorable, cardioprotective shifts among people with a trio of heart disease risk factors: high triglycerides, low HDL and an abundance of smaller, more dense LDL cholesterol. What has made niacin less than desirable are the high doses needed to produce these effects (in excess of 1,000 mg per day) and the potentially uncomfortable skin flushing that follows 15 to 60 minutes after ingestion. (Niacin's nonflushing counterpart niacinamide does not provide the same cardiovascular benefits.) Time-released niacin formulations, gradually increasing daily doses up to a maximum tolerable dose and taking niacin with meals all can cool down the flushing. Preceding niacin with a "baby" aspirin tablet, which blunts the flushing effect, may also help. High-dose niacin therapy should be monitored by a physician.

An alternative form of nicotinic acid that does not cause flushing, Inositol hexaniacinate, can be helpful for people suffering from intermittent claudication. This condition causes leg pain with exercise due to poor blood flow to the legs. Dilation of the blood vessels caused by the inositol hexaniacinate relieves this condition to some extent, allowing the patient to walk farther with less pain.
 

Natural sources

Tuna is one of the best sources of niacin, but many foods contain it. Most processed grain products are fortified with niacin, as well as other B vitamins. Although niacin is not destroyed by cooking, it does leach into water, so cooking with minimal liquid best preserves it. The amino acid tryptophan is widely found in foods high in protein, and about half of the tryptophan consumed is used to make niacin. Cottage cheese, milk, fowl, and tuna are some of the foods that are highest in tryptophan.

Supplemental sources

Niacin can be purchased as an oral single vitamin product. A balanced B complex supplement is preferred over high doses of an individual vitamin unless there is a specific indication. Supplements should be stored in a cool, dry place, away from light, and out of the reach of children.

Deficiency

A serious deficiency of niacin causes a condition called pellagra. Once quite common, it has become rare outside of areas where poor nutrition is still the norm. The symptoms include dermatitis, dementia, and diarrhea.  Milder deficiencies of niacin can cause similar, but less severe symptoms. Dermatitis, especially around the mouth, and other rashes may occur, along with fatigue, irritability, poor appetite, indigestion, diarrhea, headache, and possibly delirium.

Risk factors for deficiency

Severe niacin deficiency is uncommon in most parts of the world, but some people may need more than the RDA in order to maintain good health. Vegans, and others who do not eat animal protein, should consider taking a balanced B vitamin supplement. Others that may need extra niacin and other B vitamins may include people under high stress, including those experiencing chronic illnesses, liver disease, sprue, or poor nutritional status. People over 55 years old are more likely to have a poor dietary           intake. Certain metabolic diseases also increase the requirement for niacin. Those who abuse nicotine, alcohol or other drugs are very frequently deficient in B vitamins, but use of niacin with alcohol can cause seriously low blood pressure. A health care professional can determine if supplementation is appropriate.

Precautions

Niacin should not be taken by anyone with a B vitamin allergy, kidney or liver impairment, severe hypotension, unstable angina, arterial hemorrhage, or coronary artery disease. Supplemental niacin can exacerbate peptic ulcers. Diabetics should use caution as supplements of either niacin or niacinamide can alter medication requirements to control blood glucose. Supplements can raise uric
acid levels, and aggravate gout in people with this condition. Pregnant women should not take high doses of niacin, or any supplement, except on the advice of a health care provider.

Health care should be sought immediately if certain symptoms occur following niacin supplementation. These include abdominal pain, diarrhea, nausea, vomiting, yellowing of the skin, faintness, or headache. Such symptoms may indicate excessively low blood pressure or liver problems. Heart palpitations and elevated blood sugar are also potential effects.

Side effects

High doses of niacin can cause a harmless, but unpleasant, flushing sensation and darkening of the urine. The "no-flush" form can lessen this complication.

Interactions

Niacin supplements should not be taken by anyone on medication for high blood pressure, due to the potential for hypotension. Isoniazid, a drug used to treat tuberculosis, inhibits the body's ability to make niacin from tryptophan. Extra niacin may be required. Supplements may also be needed by women taking oral contraceptives. Concomitant use of niacin with statin class drugs to lower
cholesterol can cause myopathy. Cholestyramine and cholestipol, older medications to lower cholesterol, should be taken at a different time than niacin or they will reduce its absorption. Transdermal nicotine used with niacin is likely to cause flushing and dizziness. Carbamazepine, an antiseizure medication, is more likely to cause toxicity in combination with niacin.

If you have a family history of heart disease and/or basic cholesterol numbers that are suspicious, ask your doctor about having specialized tests to determine cardiovascular risk.  Take niacin only under a doctor’s care; it can cause liver damage in the large doses that are necessary to be effective.