You know, I was a bit concerned about that myself because I started the Lugol's right after coming off of the HW cleanse - I think I did have somewhat a lack of good bacteria immediately after the cleanse so took some probiotics for about a week, then forgot about them. I have been on the Lugol's about three months now and my digestion is better than ever so I do not think that it does harm it. However, you might want to post your question in the iodine forum, I know I have read that it does not somewhere on there but cannot remember which post to link you to, sorry.