The finding, from a team at Imperial College London, could mean that the timing and design of the vaccines may have to change.
The researchers, working on vaccines for lung infections, have shown for the first time that the previous infection history of an individual greatly affects the duration and severity of subsequent infections.
This means their development takes no account of the potential impact that previous infections may have had on the individuals who are to be vaccinated.
Lead researcher Dr Tracy Hussell said: "This is quite unrealistic when you are trying to vaccinate a human population which would have seen a number of infections at various stages of their lives."
Dr Hussell and her collaborators have been working on Respiratory Syncytial Virus (RSV).
They have shown that mice which have been previously infected with influenza do not suffer the characteristic symptoms of RSV - weight loss, illness and lung eosinophilia - when they are subsequently infected with RSV.
Dr Hussell said: "What we have found is that one viral infection in the lung profoundly changes the way we respond to an unrelated infection at the same site.
"By 'educating' itself, the immune system actually improves the way we respond to a second unrelated infection."
At present, there is no human vaccine for RSV, but scientists are carrying out work on animals.
Vaccine withdrawn
A vaccine containing an inactivated, dead form of the RSV virus was tested on children in the 1960s.
But it had to be withdrawn following the deaths of some vaccinated children who were infected by RSV in the community - illustrating the point that vaccines do not work in the same way for all who take them.
The youngest children with the less mature immune systems were those who were found to be most at risk.
However, the older children who had more experienced immune systems were not so badly affected.
Co-researcher Dr Gerhard Walzl said: "Presumably, the older children would have encountered a number of infections in their lungs before they received the vaccine.
"This will have protected them from the harmful effects of the inactivated RSV vaccine."
RSV is the most common cause of viral bronchiolitis, an inflammatory reaction in the lower airways, in infants and young children in the western world.
It may lead to asthma and allergies in later life. A life-threatening infection, RSV affects very young children because of their immature immune system, and because their lungs are not fully developed.
Elderly people are affected too, because of their waning immunity.
The research is published in the Journal of Experimental Medicine.