I just had both of my male rat terriers nurtured, first time for either one to be in the Vets office now they both are shaking their heads. Both of them have clean ears could they have picked up something. Neither one stayed over night?? Also my female dog who was at home has taken up shaking her head as well just not as bad. Changed there dog food type but not brand?? I see there could be several reasons for this. But I feel this is something they might have gotten from the Vets office a lot of animals pass through there on any given day. We live in a rual area and my dogs are fenced in and have little contact with other dogs. The weather has turned usseasonal warm here in La and wonder if it was allergies?? I tried a half of allergy pill for both but didn't seem to help. Have to return to Vet in am to have stitches out not so sure about this now. Neither has ever been sick.

I admit I had to look up Rat Terrier, we don't have them here in Australia, very cute dogs.

Infection is a strong possibility, they are fairly common in dogs and easy to treat.
Ask you vet to do an ear swab. With a swab they take a sterile bud and wipe the inside of the dogs ear, the swab is then smeared on a plate and examined under a microscope.
If there are any mites inside the ear, they will show up on the scope.

Infection can be a little harder to diagnose but it is usually accompanied with redness, heat, swelling, foul odor, black discharge... they may have all or one of these symptoms.

There ears could be itchy.. Do they have an unusual oder? Ear Mites STINK! Even if there isn't any gunk, but if you had ear mites, gunk would have built up fast and would be smell and very dark, almost tar-like.

If there ears are red or bright pink, definitely an infection.

The only thing I can think of is dry itchy ears, in which case, get ear cleaner and clean them. Don't clean with a dry cotton swab, they strip the ear of its natural oils. Get a liquid ear cleaner or ear wipes and clean them out. The moisture might help help them from shaking their heads.

Definitely go to the vet if you have suspicion that this came from them...

Good luck

Since, you are already taking them to the vet for their stitches to be removed, definitely ask to have their ears checked.

How old are they? If you are having them neutered, are they still young pups? I ask because my Dobie went through a head-shaking/jaw scratching phase when her back teeth were coming in.

If they have a clean bill of health, then you might want to look for environmental causes. The main thought that comes to mind is something causing a noise that they can hear but you can't. Wiring is one possibility or the ballast of some of the modern energy saving light bulbs can sometimes cause a high-pitched whine. Insect activity is another thought.

Good luck.