The Shulchan Aruch mentions that one should not daven in the presence of a dog. Is there an exception or leniency made if a blind person accompanied by his dog walks into the shul minyan to daven? (the blind person, that is. Although, perhaps, the dog may be davening, as well.)
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Igros Moshe 1:45 says it is permitted, as if not the fellow will be unable to ever come to Shul. However it is preferable to leave the dog at the door in order not to scare the congregants.
I have personally seen a seeing eye dog in a Shul on more than one occasion.