Unfounded and unjust
I think it is now established that the study design was a small case
series report and a perfectly good one, according to Dr Ben Goldacre. 
But the Wakefield et al paper did not state a hypothesis, a flaw
considered serious enough for Trisha Greenhalgh to invent one,
“The administration of MMR vaccine to infants increases their risk of
developing (a) a particular pattern of inflammatory damage in the gastro-
intestinal tract and (b) autism or an autism-like syndrome.” 
In her 2004 critical appraisal of the paper, Professor Greenhalgh
then asks herself whether this design was an appropriate way to test the
hypothesis. No, she says, “if the hypothesis was that there is a causal
link between MMR and autism-bowel syndrome, this study design was
incapable of proving that link one way or the other.” And the knowledge
that case reports do only provide weak scientific evidence for such causal
links, was probably why, in their paper, Wakefield et al stated,
“We did not prove an association between measles, mumps, and rubella
vaccine and the syndrome described.”
And why, in the last paragraph, they wrote,
“We have identified a chronic enterocolitis in children that may be
related to neuropsychiatric dysfunction. In most cases, onset of symptoms
was after measles,
mumps, and rubella immunisation. Further investigations are needed to
examine this syndrome and its possible relation to this vaccine.” 
 Ben Goldacre. Don't dumb me down. We laughed, we cried, we
learned about statistics ... 8 September 2005.
 Professor Trisha Greenhalgh. Analysis of Wakefield MMR study asks
why flaws weren't spotted by Lancet editors. April 2004.
 Early report. Ileal-lymphoid-nodular hyperplasia, non-specific
pervasive developmental disorder in children.
A J Wakefield, et al. THE LANCET • Vol 351 • February 28, 1998 637.
Competing interests: No competing interests