In 2005, Rolling Stone, along with Salon, published a ludicrous hit piece claiming that the CDC enagaged in a massive consipiracy to cover up the link between the vaccine preservative thimerosal and autism. The piece, titled "Deadly Immunity", was written by none other than Robert F. Kennedy Jr.
It was standard, unbelievable conspiracy-theory fare (for example, treating perfectly routine decisions as evidence of something sinister) and was based on pseudoscience that was already completely discredited at the time and has since been further discredited. Salon eventually wound up retracting the article, but Rolling Stone still hasn't (there were claims that they retracted it in 2011, but the article reappeared later that year and RS explained that the disappearance was an accident related to site reorganization); the article is still available, although behind a paywall.
UPDATE
Link to the story (paywall)
Seth Mnookin's discussion of the disappearance and repost