The most simplistic question would be "Are vaccines safe?"
The best answer to that would be "No, they are not."
There is nothing inherently safe about injecting foreign substances, especially potentially infectious ones, into a body.
There is also nothing safe about succumbing to a fatal parvovirus, or being an outdoor cat at high risk for feline leukemia. We have to weigh the relative risks of each in order to make some determination of what risks we are willing to accept.
We incur risks all the time. Some of the risks are real; some are only potential or theoretical. Real risks can be likely or only possible. One of the real risks of vaccination is pain. It is pretty much guaranteed that when you put a needle through a pet's skin, there will be some pain. It is real and it happens in almost every instance when a vaccine is administered.
Another real risk is an anaphylactic or "acute shock" reaction. A pet with a hypersensitivity to the vaccine or one of the components of the vaccine can go into life-threatening cardiopulmonary arrest and die. This is a real risk, but it is only possible, not likely (in fact, it is very, very rare).
Other vaccine responses are less dramatic; a pet might feel dull, run a fever, be off food, have soreness at the site of the injection, or just generally feel "blah" for about 24 hours after getting vaccinated. This, too, is a real risk, but it is a likely risk as opposed to the risk of anaphylaxis, which is only a possible risk.
Cats run a very real risk of developing cancer at injection sites. This phenomenon was first noticed in the 1980's after the advent of the feline leukemia vaccine. Research into this potentially deadly problem has identified inflammation as the culprit; any injection (not just of vaccine material) that causes inflammation can result in the future development of a particular type of tumor called a fibrosarcoma.
These tumors are very difficult to treat successfully. Initial treatment consists of very wide and deep resection of the tumor and surrounding tissues. Three centimeter margins are the minimum recommended in all planes. This means that the surgeon must get tissue three centimeters deep to the tumor as well. If you picture a tumor on the back of a cat's neck or shoulders, which is typically where vaccines were given, you can see that going three centimeters down into the shoulder or neck of the cat becomes problematic. There is bone involved, as well as a lot of muscle. There is no way to realistically remove these margins and leave enough tissue for the cat to function. If the tumor is over a limb, margins are attainable by amputating the limb. This is the treatment of choice for fibrosarcoma in the cat.
Needless to say, we want to avoid this at all costs. We can take reasonable measures to decrease the risk of fibrosarcoma tumors on cats by being careful about what is injected, decreasing the number of vaccines given, and using vaccines that elicit the least inflammation possible when they do need to be given.
In general, vaccines that contain adjuvants elicit more inflammation than those that do not. Adjuvants are compounds that are put into the vaccine to deliberately irritate the immune system and cause a greater immune response. They do this, in part, by causing inflammation. At this writing, we think that the safest vaccines for cats are non-adjuvanted.
Other things have been implicated in fibrosarcoma formation in both dogs and cats, including Program injections and microchip implants. The rate of reactions is low, but it is a risk nonetheless and something of which cat parents should be aware.
The estimated rate of fibrosarcoma formation is one tumor per ten thousand injections given. If your cat only receives 1 injection in his lifetime, he has a 1 in 10,000 chance of getting a tumor. This sounds very low until you start counting up all of the potential injections, especially vaccines, that your cat might receive over a lifetime. If your cat is vaccinated every year for distemper and feline leukemia, and maybe rabies - that is approximately 35 injections over a lifetime. The risk increases to 35 in 10,000 or a 1 in 286 chance. Add a Program injection every 6 months for 10 years (20 more injections) and the risk increases to 1 in 182. Suddenly the numbers are not so comforting.
Another risk is actually getting the disease, at least in a mild form, from the vaccine. This happens most commonly with intranasal or intraocular vaccines, and it is thought to happen because the vaccine is being given via the natural exposure route for the disease. The symptoms are generally mild and self-limiting.
One potential risk of vaccination that is just starting to be recognized and explored is the induction of immune-mediated diseases by repeated vaccination. A positive correlation has been shown between immune-mediated hemolytic anemia (IMHA) in dogs and recent vaccination (within the preceding 4 weeks). The incidence of IMHA post-vaccine is very low. Studies are going on currently, looking into whether there is a correlation between vaccinations and arthritis, allergic disease, and pemphigus.
So do these risks mean that we ought to stop vaccinating altogether? No. We have established control over epidemic diseases using vaccines. Parvo is not the killer that it once was. Both feline and canine distemper are common in unvaccinated populations, rare in well-vaccinated ones. Vaccines have their place.
We do have to be rational about their use, and think about what we are doing. We have to question the long-held beliefs about what we do with your pets and why we do it, what the real and perceived benefits are, as well as risks. We need to base our decisions on evidence as well as experience.