We don't yet fully understand the highly sensitive interplay between fight and tolerance in our immune system. What consequences our interference from outside bears is impossible to predict. Another important issue is the purity of the vaccine. Despite the utmost cleanliness strived for, it is technologically impossible to exclude all possible risks of contamination entirely. Virus contaminated cell cultures are a significant problem of the bio-industry.
Live vaccines possess a higher risk of contamination with micro-organisms than other vaccines.
Ontogenetic viruses are, for example, present in mammalian cell strains used in vaccine production. Particularly when these modifications are only minor, like localized mutations, the danger of back mutation into a pathogenetic virus is possible. The difference, for example, between the Sabin strain and one of the virulent poliomyelitis strains is only the addition of one nucleotide. Another drawback of live vaccines lies in their possibility of complementation or recombination with closely related wild strains or vaccine strains. The likelihood and possible consequences of this are wholly unknown.