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This can be a controversial area, but I'll give my opinion. I'm only talking about Coccidiosis and Marek's. You can get vaccinations for other diseases that can have longterm effects, but these are not usually available from the hatchery for us.
Many vaccinations can be given and the chickens remain" certified organic". You need to check with your certifying authority to see which ones may affect their organic certification.
Sometimes the vaccinations are given with needles, which can have obvious effects, especially if the needle does not go in right. Many are given in a spray at the hatcheries. Either the vaccination is breathed in or they injest it when they preen their down. This would be less stressful to them than a needle.
I'm not aware of any longterm negative effects of the vaccines themselves.
If you get your chicks vaccinated for Coccidiosis, them you should not feed medicated feed for the first three weeks or so or you can negate the effects of the medication.
One really controversial part of the medicated feed is the withdrawal period for egg production or butchering them for meat. Some say there is no withdrawal period for either if the chickens eat medicated feed. Some say there is up to a four week withdrawal period. The European Union goes by parts per million in the eggs or meat. I don't have the technology to test my eggs or meat for parts per million, so that did not help me much. The best I can interpret the legalese on the government sites, they say it has not been proven to cause problems. They sometimes point out that they do not say it has been proven to not cause problems. There is a difference in the meaning. I go by a statement I read by a bird veterinarian. He tended to think that it was not a huge problem since the intestinal walls do not allow much Amprolium to be absorbed, but due to the possibility he recommended a one week withdrawal period. But from what I can see, even the experts cannot reach consensus. What chance do I have?
This is pretty much the extent of my opinion and knowledge. I really don't consider either to have any longterm downside.