Amitriptyline is a tricyclic antidepressant and like other
tricyclics they can have severe anticholinergic effects
such as weakening the LES and causing GERD. I was on
Nortriptyline for only a couple weeks and it caused me
extreme reflux problems while I was taking it.

I was under the impression that LES function would return
after stopping the medication (have you heard otherwise?).
You should talk to your doctor about changing medication
to something with less anticholinergic effects. One of the
newer selective serotonin reuptake inhibitors (SSRIs) perhaps?

Please let us know if the doctor thinks the LES effects from
this drug are permanent. I was under the impression that they
shouldn't be.

Mark.