A clean but smelly toilet almost certainly means that you've got a leak between your toilet and the closet flange. The closet flange is the opening in your bathroom floor where the toilet is mounted that leads to the sewer system. Normally the toilet and flange are sealed together with a wax ring. Over time, these wax rings degrade, which allows sewer gases, and sometimes water, to escape from your toilet. Repairing a smelly toilet should be done as soon as possible, as sewer gas can build up and become dangerous.
Turn off the water supply for the toilet. This is usually located on the wall behind the tank. Rotate the circular water supply valve clockwise to turn off the water.
Flush the toilet to remove any water inside. Wipe up any excess with the towels and sponge. Then unscrew the plastic water supply hose coupling on the bottom of the toilet and the bolts at the bottom of the tank. Lift the tank off the back of the toilet and place it out of the way.
Remove the plastic caps on the bolts at the base of the bowl. Unscrew the tank bolts with the adjustable wrench. Remove the bolts and washers.
Run a utility knife along the caulk between the bowl and the base (if present). Gently rock the bowl from side to side to loosen it. Lift the toilet bowl up and away from the flange.
Place a towel on the floor. Turn the toilet bowl upside down and place it over the towel. Clean off the bottom of the bowl. Remove any traces of wax with a putty knife.
Clean the closet flange in the floor. Remove any traces of putty with the putty knife. Wipe up any soil, mould or mildew with the rags and bathroom cleaner. Press a new wax ring into place and then slip two new flange bolts into the closet flange.
Roll out a bead of plumber's putty. Press this into place on the bottom lip of the toilet bowl. Turn the bowl over and align it so that the exit hole on the bowl is lined up with the closet flange in the floor. At the same time, the two flange bolts must line up with the holes in the bottom of the toilet. Have someone help you if necessary.
Lower the toilet over the flange and press into place. Slip the washers over the flange bolts and secure with the flange nuts. Tighten the flange nuts first by hand and then give an additional turn on each side with the wrench.
Replace the tank on the back of the bowl. Drop the screws into the bottom of the tank and secure with the nuts from underneath.
Wrap the tank inlet with plumber's tape. Secure the plastic coupling from the water supply hose and tighten with the wrench. Restore the water supply. Flush and check for leaks.
Insert the tube of caulk into the caulk gun. Trim off at the 1/4-inch mark at the end. Caulk around the base of the toilet.