Recently our daughter was told she should probably get a Hepatitis B immunization. We have no problem with the immunization theory, and in certain instances would certainly have our children and ourselves immunized. But over the years, we have concluded that shooting a bunch of microbes into a person might not be such a good idea, and may have something to do with the auto-immune diseases we see so much of today.
I am neither a doctor nor the son of a doctor (though my father, before he retired, was a pharmacist, if that's worth anything) so my opinions of things medical shouldn't be taken that seriously. Therefore, I can't really give you an authoritative opinion on the pros and cons of immunization. However, I can say that you would be very hard pressed to find credible sources in Torah literature discouraging it.
Here's one possible explanation why that might be: our lives and our health, we believe, are in God's hands. Of course, we're commanded to take steps to protect those precious gifts, but our fate, ultimately, lies beyond our control.
The complex world in which we live offers us nearly an infinite variety of possible health choices: should we or shouldn't we eat baked or fried potatoes...take a healthy walk in the sunshine or perhaps it's too bright...visit a doctor or a chiropractor or an acupuncturist for that back pain and so on...forever. We can't possibly act on every warning and risk (for one thing, we'd never eat again: over the past year, it seems, there have been studies conducted that both warn against and promote just about every kind of food imaginable). And proper research into the relative merits of every option would leave us without a minute free for the performance of the other 612 commandments!
So how are we to make our decisions? How are we to properly observe the mitzvah to guard our health? The Torah teaches us a general rule based on the rather odd-sounding source "God is the protector of fools." (Psalms 116; 5) Believe it or not, the Talmud itself, in many places (see, for example, Yevamos 12b and Avodah Zarah 30b), cites this verse to demonstrate that when a potential risk is commonly ignored (and the risk itself is somewhat distant) one may rely on God's good offices for protection. We, who are "foolish" by virtue of our involuntary ignorance, can expect the Master of the universe to guide us as He sees fit.
Of course, this logic doesn't apply to known and acute risks, like smoking or driving without seatbelts. For these, we must take full responsibility.
Thus, however, the general rule: since we must live full Torah, private and professional lives and can't possibly take every imaginable precaution, we must rely on God to silently guide us along the path He deems best for us.
It's quite possible, then, that any potential risks associated with universal inoculation programs are distant enough to fall into the category of "God is the protector of fools."
I would also add that, in choosing not to inoculate yourself or your children you are making a decision not only for yourself, but for the rest of society as well. Every person left unprotected from polio or whooping cough etc., is one more potential source for the spread of that disease. While you might be justified in taking that risk for yourself, you are also, in a sense, arbitrarily imposing your beliefs on the members of your community.