a) high triglcyerides
b) low HDL (but this takes awhile according to several reports on The Peak Testosterone Forum).
c) high counts of small LDL
High dose niacin will generally tremendously lower triglycerides, decrease LDL some and and increase HDL. The effect is powerful enough that it can improve erectile dysfunction in some men with the above lipid problems, something I discuss in detail on my page on Niacin and Erections.
I will start with the dosages mentioned by two physicians who have actually been on the field reversing arterial plaque (atherosclerosis) with niacin. I have what I think is an interesting page about two of these men that I call “The Plaque Reversers” here: Doctors Regressing Atherosclerosis. And we’ll also cover the dosage for Niaspan, the prescription timed release form.
1. Dr. Davis. This best-selling author used niacin therapy as one of several supplements (including fish oil and Vitamin D) to reverse arterial plaque. He is one of the three doctors that I call the “The Plaque Reversers”. (You can read more about them here if you are interested: Doctors Regressing Atherosclerosis.) Dr. Davis says that in his experience the no-flush niacin is next to worthless and provided almost no lipid changes whatsoever. In his book Track Your Plaque he wrote that “doses at 1000-2000 mg are very effective, depending on your weight and some genetic factors. Niacin is best prescribed by a doctor who has experience in dealing with the peculiar effects of niacin (most of them harmless), like feeling hot and itchy.” 
2. Dr. Gould. Another physician that is one of what I call the “Plaque Reversers,” is Dr. K Lance Gould. In his book Heal Your Heart, Dr. Gould writes:
3. Niaspan Directions. All the big pharmaceutical sites that I looked at recommended that you start with 500 mg daily of Niaspan for the first four weeks; 1,000 mg per day the next four weeks; 1,500 mg per day for the next four weeks; and plateau at 2,000 mg per day thereafter. Note that Niaspan is timed release and immediate release is considered less liver toxic. Please note that I am NOT pushing Niaspan but just using it as an example. Notice the similarity with Dr. Gould’s strategy above, i.e. steadily increasing the dosage.
CONCLUSION: Both doctors recommend rougly 1,000 mg per day (and in some cases up to 2,000 mg) of niacin in order to actually regress plaque. Dr. Gould has a particularly appealing protocol in my opinion, because he is apparently able to avoid much of the rather disturbing flushing effects associated with it.
I am trying to avoid taking high dose niacin myself but have considered it. My approach was going to be to first choose my ApoB Targets and HDL, LDL and Triglyceride Targets. Actually, I have already done this step and am fairly close to all of these numbers simply by following a Low Fat Diet.. However, I would like to improve my numbers by about 10%. So I was simply going to increase my niacin dose until I achieved those goals. I have a feeling that I would have to take signficantly less than 2 grams per day to achieve my goals.
1) Track Your Plaque, by William Davis, p. 94.
2) Heal Your Heart, by Dr. K. Lance Gould, p. 176-177.