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Dr. Nicholas Dodman, veterinary behaviorist at Tufts Veterinary School, talks in one of his books about thunderstorm phobia. He's had minimal sucess treating this condition but did have results with the use of an SSRI, like Paxil or Prozac and rubbing the dog with dryer sheets. Don't recall all the details. The book I believe was "The Dog Who Loved Too Much" or something like that.

As Betsy suggests, medications are usually used in conjunction with a behavior plan to treat phobias and other OCD disorders so your vet probably might recommend a behaviorist.

Keep us posted.
 
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