Parents of autistic children felt stress, guilt and frustration as a result of the controversy over the MMR vaccine, according to a study.
Uptake rates for MMR were hit by the scare
Doubts were raised over the safety of the vaccine after Dr Andrew Wakefield claimed he had found a link between it and autism.
His research, first published in 1998, has since been widely discredited.
The Medical Research Council in Glasgow said the controversy put parents of autistic children under great pressure.
During the early years of the decade concern about a possible link with the triple vaccine for measles, mumps and rubella was at its height and the number of children being vaccinated fell from 94% to 87%.
Research led by Dr Wakefield claimed the jab was linked to autism, but much larger studies have since ruled this out.
The MRC's social and public health sciences unit undertook 10 focus group discussions across the UK between 2003 and 2005 involving 38 parents of children with autism.
Dr Shona Hilton and her colleagues found that some parents had experienced "agonising uncertainty" over whether the MMR vaccine may have provoked their child's autism.
Many wondered whether they were to blame for their child's condition or felt they had "let their children down" by deciding to vaccinate.
Even those who felt that their child's autism was not linked to the MMR vaccine, either because of family history or because they had avoided vaccination, had suffered as a result of the ambiguous advice they felt that they had received.
Dr Hilton said: "It is clear from a review of the literature that there has been a lack of follow-up of the impact of this health scare on those likely to be most directly affected - those living day in and day out with children with autism.
"These parents in particular have been under a huge amount of stress about the possible impact of their decision to vaccinate or not."