In general, vaccines are monitored for their immediate safety. So if a significant vaccine side effect occurs within days or a few weeks of administering the vaccine, then it will likely be noticed by the Vaccine Adverse Event Reporting System (VAERS).
The VAERS program accepts reports of potential vaccine side effects from both individuals and healthcare professionals. The reports do not have to prove that the vaccine caused the problem. The researchers at VAERS simply want to know about any medical issues that occurred in close proximity to receiving vaccines. Information about VAERS can be found at http://vaers.hhs.gov/. If you would like to report a vaccine side effect, you can fill out the VAERS information online or print out a form and mail it to the organization.
Since 1990, the VAERS program has received well over a hundred thousand reports of medical events after vaccines. Over 85 percent of the reports are for mild and/or transient problems, such as fever, pain, or mild irritability. The remaining 15 percent include more serious experiences, such as being admitted to the hospital or requiring surgery.
The VAERS program was responsible for noting that the rotavirus vaccine approved in the late 1990s had a significant side effect. After a million doses of the vaccine had been given, a slight increase in the risk of intussusception was noted. Given that intussusception is a dangerous condition that often requires surgery and can occasionally lead to death, the CDC made the decision to withdraw the vaccine from the market. We view this decision as mark of confidence in the system: a problem was found quickly, and the vaccine was removed.
However, to our knowledge, there is not a good system for monitoring possible long-term side effects from vaccines. If a child develops juvenile diabetes five years after his last set of vaccines, most physicians are not likely to think of reporting that diagnosis to the VAERS system as a complication of vaccination. Even if they did, they would probably have a hard time proving this were so. However, some people have felt that certain autoimmune diseases, such as diabetes or multiple sclerosis, are linked to vaccines.
Possibly the best way to investigate these types of hypotheses is to use population studies. Several Scandinavian countries and a few large HMOs have the data to see if there is an association between a certain vaccine and a certain disease years later. So far the studies have not supported any theory of harm. We have to admit, though, that the research in this area is limited.