My 2009 physical was an interesting one. I got a call from the receptionist who read my results and said, "Your results were all acceptable but we are a little concerned with your HDL readings. You might want to take some more omega-3's."
What was my HDL that was scary? 32. That's right - 32. Now most Americans with a reading of 32 should be scared, even terrified. If you have "normal" cholesterol on a typical Western diet (180-200), you need solid HDL numbers of 40 and above to help protect your arteries.
But should I be scared? No, and I'll tell you why: my total cholesterol number was 127. (My blood pressure - and remember I'm dang near 50 - was 110/70.) I'll state this again: there is virtually no heart disease in individuals with cholesterol less than 150.
The receptionist meant well, but let me explain just how ridiculous her statement was. Consider the Tarahumara Indians: they have no heart disease, no hypertension and virtually undetectable cancer rates. They are exempt from virtually all of the modern health plagues of modern societies and shame us with the billions of dollars spent on research and health care.
So what is the HDL for a Tarahumara male? It is even lower than mine: 26.  Think of the irony: one of the healthiest supercultures on planet earth has supposedly horrible HDL. The truth is that their HDL is beautiful, because it goes along with a total cholesterol reading of 136 (for males). [Triglycerides for males were 123 and LDL 87.]
And that's why I'm proud of my lipid readings: they are very comparable to the disease-free Tarahumarans. The Tarahumarans are not the only culture where this holds true by the way. Dr. Ornish, in his groundbreaking The Spectrum, points out that the China Study found that heart disease in the United States was seventeen times higher in men than in parts of China. One of the primary reasons was the fact that in these parts of China, cholesterol averaged 127 whereas in America it was 200. 
Dr. Ornish, again in , explains that on a Low Fat Diet, HDL does decrease and the reason is that HDL's purpose is to usher away the bad cholesterol, LDL, to the liver for metabolization. And if you have less bad cholesterol, due to a Low Fat Diet, your body lowers its HDL count because you do not need as much HDL any more. Furthermore, on a Low Fat Diet one's HDL decreases by about 9% but LDL decreases by a whopping 40%. 
The bottom line is that critics love to assault Ornish and other Low Fat Diets, but the truth is that these diets work. I actually don't eat a perfect Low Fat Diet as I allow some nuts, a little canola oil and occasional meat - about twice a week - along with some dark chocolate. (I even eat an egg yolk, which is filled with cholesterol, about three times per week for the lutein, etc.) However, when all is said and done, my nutritional profile is simialr to the Tarahumarans, who eat 12% protein, 75% carbohydrates, 13% fat and 2% saturated fat and the effect has been overwhelmingly positive in my life as far as I can tell.
1) Amer J of Clin Nutr, 1978, 31:1131-1142, "The Plasma Lipids, lipoprotein and diet of the Tarahumara Indians of Mexico"
2) The Spectrum, Dr. Dean Ornish, p. 210.
3) The Spectrum, Dr. Dean Ornish, p. 207-208.