His comments on vaccinations was ill informed and quite frankly reckless as hell!
http://www.snopes.com/medical/disease/cdcwhistleblower.asp
Vaccination data were abstracted from immunization forms required for school entry, and records of children who were born in Georgia were linked to Georgia birth certificates for information on maternal and birth factors. Basically, no significant associations were found between the age cutoffs examined and the risk of autism. I note that, even in the "reanalysis" by Brian Hooker, there still isn't any such correlation for children who are not African American boys
So is Hooker’s result valid? Was there really a 3.36-fold increased risk for autism in African-American males who received MMR vaccination before the age of 36 months in this dataset? Hooker [performed] multiple subset analyses, which, of course, are prone to false positives. As we say, if you slice and dice the evidence more and more finely, eventually you will find apparent correlations that might or might not be real. In this case, I doubt Hooker's correlation is real.
There's no biologically plausible reason why there would be an effect observed in African-Americans but no other race and, more specifically than that, in African-American males. In the discussion, Hooker does a bunch of handwaving about lower vitamin D levels and the like in African American boys, but there really isn't a biologically plausible mechanism to account for his observation, suggesting that it's probably spurious. There are multiple other studies, many much larger than this one, that failed to find a correlation between MMR and autism.
What [Hooker] has done, apparently, is found grist for a perfect conspiracy theory to demonize the CDC, play the race card in a truly despicable fashion, and cast fear, uncertainty, and doubt about the CDC vaccination program, knowing that most of the white antivaccine activists who support [him] hate the CDC so much that they won't notice that even Hooker's reanalysis doesn’t support their belief that vaccines caused the autism in their children.
Read more at
http://www.snopes.com/medical/disease/cdcwhistleblower.asp#mAtu53il8KEppg6X.99