I have been having chronic diarrhea, bloating and pain for the last year or so. I had been travelling in Spain and was very sick there. However, nothing has shown up in my stool except for endolimax nana, which is considered to be non-pathogenic. We have looked in to other possibilities (i.e. Crohn's, Celiac) but no diagnosis there either. I started a course of flagyl, which made me so sick that my Doctor decided to stop treatment as she said that it was 'shot in the dark' treatment. While I was on the flagyl, however, my symptoms went away. I just had vertigo and nausea so bad that I couldn't function. Should I try doing another course of flagyl again, now that we've ruled other diseases out, or is it not the right treatment for me?

They used to teach us that Endolimax and other protozoa didn't cause disease, but I've treated plenty of people with these "non-pathogens" and symptoms of bloating, diarrhea and abdominal discomfort, so I think the textbooks are wrong about this. If you have trouble taking metronidazole (Flagyl), you can try paromomycin instead. People rarely have problems with it in my experience.