Yes, yes, yes!!! Puppies are like children -- if you act like something is to be scared of, they WILL pick up on it from you and they WILL be scared of it! So make sure the appointment is nothing but positives!! Lots of hugs, belly rubs, kisses and treats!! We distract our puppies with treats and head scratches while getting their injections - and most of them NEVER notice or flinch. The ones that do are *usually* the ones with the owners in the background wincing and saying "omg you poor baby!!!!!!", of course the puppy then reacts to the owner and the shot by association.
You can vaccinate puppies as early as 6 weeks. "Normal" protocol (as I was taught in school, and as we practice at my clinic) is they get one round of vaccines at 6-8 weeks, another at 9-11 weeks, another at 12-14 weeks, and their final set of vaccines (including rabies) at 15-18 weeks. A LOT of breeders will vaccinate as early as 3 weeks, which is entirely way too young. The reason why we have to do a few rounds of vaccines is because there is no exact known time frame of when the mother's antibodies wear off in the puppy, so you do a few rounds to make sure the puppy is adequately covered. Bordetella (kennel cough vaccine) should not be done earlier than 9 weeks, either, and rabies "legally" can't be given any earlier than 15 weeks (depending on your state).
It is a little concerning that you were allowed to take a puppy away from it's mother that young (around 4-5 weeks of age?) so I would definitely recommend discussing that with your vet.
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