Can Flagyl cause foul smelling stools? After I finished a 7 day pulse I have that problem real bad. Also vaginal too. I know Flagyl can cause more yeast which I always have in abundance but my question is - did I take the flagyl for too short a time and caused a bowel infection??? Or maybe it's more likely that I got a killer candida infection in my colon? Sorry to be gross but just wondering if anyone has had that problem and what did they used to get rid of it? I am taking 1 - 100mg diflucan pill a day (which I always have to take anyway) and probiotics.