When it comes to studies of vaccine side effect there one thing that very worrying. When a new vaccine enter the market there is testing for side effects. Those studies actually do find side effects and the Center of Disease Control should be a trustworthy source for reporting them.

It turn out different vaccine have quite different side effects. They didn't find any Nausea, vomiting, diarrhea, or abdominal pain as a side effect in the Hepatitis A vaccine but 1 of 4 people who take the HPV--Cervarix vaccine get them. Maybe different vaccine work extremely differently and therefore it doesn't make any sense to generalize the risks of one vaccine to the next. Maybe the studies that list the side effects are also to poor.

Even more worrying the side effects reporting system that regular doctors use while the drug is on the market completely fails to capture the side effects that would be expected. If I remember right they find more than two orders of magnitude less side effects than would be predicted based on the studies for bringing a drug to the market.