Over time, toilets get stains that may seem impossible to remove. They are generally stains caused by hard water that create streaks down from the nozzles that refill the bowl. On occasion, if you don't clean the bowl often, you might also get a mildew ring around the bowl that is equally difficult to remove. Because of this difficulty in cleaning, the stains are sometime assumed to be permanent, but in most cases, you can get rid of them.
Remove the water from the bowl. Turn off the water by turning the knob behind the toilet, the flush the toilet to make the water go out. If it doesn't completely go out, use a plunger to force the rest out.
Soak paper towels with a toilet cleaner. Use a cleaner that has hydrochloric acid in it if the stain is an orange and brown rust stain. Other names for the chemical include HCL and hydrogen chloride. Do not use a product that contains bleach on rust stains. Use bleach products on mildew stains. If you have both issues, do not use both products at the same time; bleach and hydrochloric acid cause a reaction that produces harmful vapours. Never combine the two. If you use a bleach tablet or some other type of item that hangs in your bowl, remove it before cleaning, and flush the toilet several times to make sure it is all out.
Lay the paper towels in the bowl so they cover the stains. Apply more cleaner if they start to dry. Leave them in place for several hours and then remove.
Scrub the bowl with a bristle brush to work the cleaner around. Reapply cleaner, if necessary. Once done, turn on the water and let the bowl fill back up. Flush away the cleaner.