An example of how this film misleads
So I didn't like the movie. Though I did like a couple things the guy brought up, as it was informational (in an indirect way as you'll see).
For example,
In his diatribe against the standard "high cholesterol causes heart disease", he brought up a researcher by the name of Kilmer McCully who worked out of Harvard Medical School in the early 80's (this appears around the 1 hour 9 minute mark of the movie). The Fat Head Document correctly points out that McCully had been advocating his own research that showed that homocysteine was the casual factor in heart disease not necessarily cholesterol. This line of thinking and research has re-arisen the past couple decades after being initially shunned (this shunning was shown in the documentary as well to strengthen the viewers belief that the national health organizations like the CDC and NIH aren't reliable sources). Homocysteine centers around the idea that reduced levels of B12, B6, and folic acid (also having kidney disease and cigarette smoking) will allow for the homocysteine process to damage circulatory system and resulting heart disease.
Here's a perfect example of why I didn't like the movie, and more specifically wanted to punch the main guy in the face (I also couldn't take his obvious sarcasm and pompous attitude).
http://www.nytimes.com/1997/08/10/magazine/the-fall-and-rise-of-kilmer-mccully.html?pagewanted=11&src=pm
This New York Times article detailed the rise and fall of McCully, in it you will also see that McCully never advocated that eating a high cholesterol diet would be good for a person. In fact, if you read this section quoted from that article:
"What, then, is the diet most likely to lead to heart disease, according to the homocysteine theory? One high in animal protein and low in B-vitamins, which occur in many foods but are very easily destroyed by processing -- a diet of meat, cheese, milk, white flour and foods that are canned, boxed, refined, processed or preserved. The American diet, in other words."
So on one hand the Fat Head documentary wants to use the example of Kilmer McCully to support the documentaries message that we (general public) are being misled by the government (visa-vi the government agencies such as the NIH and CDC) in being told that high cholesterol is linked to increase in heart disease, but on the other hand the documentary chooses to ignore that McCully's findings still support the same dietary message that NIH and CDC promote, that a diet high in animal protein (or larger servings of meat) simple carbs (white flour, refined sugars, etc.) and processed foods are bad for our health.
This kind of "reporting of facts" through a documentary just pisses me off. It's this kind of behavior on the part of the documentarian that calls in to question his/her work ethic and really the legitimacy of the whole piece.