Conflicts of Interest Seem to Outweigh Our Children's Interest
The science that says vaccines are not related to autism is based solely on large epidemiological, or statistical, studies. Problems with these studies include ties to organizations connected to the vaccine program. This type of influence makes it doubtful that conclusions unflattering to these organizations would be reached. Besides containing questionable interpretations of the data, the studies all selectively eliminated subjects that did not fit their pre-determined conclusions.
These studies also frequently cite the findings of the Institute of Medicine (IOM)—which determined no causal link—and do so without mentioning that the IOM was commissioned by the CDC (Centers for Disease Control and Prevention) to issue the report on "Vaccines and Autism." The studies also neglect to acknowledge that the Committee failed to allow published toxicological data to be presented, and that a significant portion of this research was not included in the IOM’s final report.
Conflict-free investigation is of paramount importance when considering the safety of vaccines. The CDC approves, mandates, promotes, and distributes vaccines, creating opportunity for conflicts of interest.

I can think of two studies and one report off the top of my head right now which are not epidemiological which refute (and kills) the MMR hypothesis:
Bustin, from Cedillo:
"What I immediately observed was that they had forgotten to do the RT step....If you detect a target that is apparently measles virus in the absence of an RT step by definition it can't be measles virus because it has to be DNA. It's a very simple concept. At least it is to me. It's not to everyone else...[b]ecause measles virus doesn't exist as a DNA molecule in nature, they cannot be detecting measles virus."
Two clinical studies are Afzal ( http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=16555271&ordinalpos=1&itool=EntrezSystem2 .PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum) and D'Souza ( http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17015560&ordinalpos=1&itool=EntrezSystem2 .PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum)