Hi - I have a new home (2yrs old) and no matter how much I clean the master toilet it always has a bad smell. My spare bath doesn't have the same problem and it gets cleaned less. I've even tried an 'industrial' type cleaner from Lowe's, but after a few days the smell returned. I also notice yellowish stains on the calking around the base. My husband swears he is aiming correctly :) and I don't see streaks coming down from the bowl so I have to assume they are seeping in from inside. Is this possible? Any ideas what could be causing the smell and how do I get rid of it? Thanks!!

Sounds like you have a ruptured wax seal and it's not only leaking water but sewer gas as well. The solution would be to pull and reinstall the toilet after first cleaning off the old seal. Good luck, Tom

Tom has given you the most probable answer to your problem. Pull toilet, clean old wax off closet flange and toilet, reinstall toilet with new wax ring and you should be set.