It could be anything from ticks to fleas to infection! or maybe just new found way of annoying you.
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Originally Posted by millsandbones

It's better to let the vet have a look on him.

I am agree with millsandbones.I think you go to a vet.

I took Charlie into the vet today and the doc couldn't see any mites, or any infection or inflammation. Charlie was shaking his head right in front of him, and the vet said that he really shouldn't be doing that. So just to make sure there isn't an infection he gave me some ear cream/ointment to instill into his ears every other day for 5 doses.
So I guess it could be anything to absolutely nothing and that my dog is just making me worry!

Glad to hear his ears appear to be fine. Just a thought. Did the vet check his teeth? Maybe he has a retained puppy tooth that's making his mouth sore? If he'll let you, pop his little mouth open and check his teeth to be sure everything looks right, and he doesn't have any redness or swelling around a tooth, or something stuck in his teeth.

How long has it been happening? My dog did that for about 3 days then just stopped. Although it might have been because he had his ears cleaned a few days before.