Here is a quote from the Border Terrier List:
"The 'Whole Dog Journal' (May, 2000 issue) had an article on remedies for noise-phobic dogs... thunderstorms in particular. They call it a 'melatonin miracle'. They administered 3 mg of Melatonin to a large dogs and found that it absolutely helped dogs that were thunder-phobic. They suggest 1.5 mg for dogs under 30 lbs. They observed no side effects.
"They suggest you give the melatonin whenever a thunderstorm is predicted and do not wait until the dog is already extremely nervous.
"They also tried it with separation anxiety with good results on a Great Dane for a while, then it stopped working. Dogs with lick granulomas seemed to respond well also. They said it was most effective when noise is a major factor."
Here are some links about noise phobia and/or melatonin which I have not yet read:
http://world.std.com/~halberst/contrib/sad.html
http://www.peteducation.com/article.cfm?cls=2&cat=1551&articleid=2545
http://www.answersleuth.com/health/remedies/melatonin.shtml
http://www.uncc.edu/lis/library/reference/human/multis.htm
http://www.forensic-psych.com/articles/artMelatonin.html
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