You should clean fresh tomatoes thoroughly before eating them. The Food Standards Agency comments that "it's a good idea to wash fruit and vegetables before you eat them to ensure that they are clean, and to help remove germs that might be on the outside." If you do not cook or eat your tomatoes immediately after cleaning, store them at room temperature. Fresh tomatoes should not be stored in the refrigerator, because cool temperatures will diminish the flavor.
Rinse the tomatoes with cool water.
Scrub the exterior of the tomatoes with a dish brush gently. The exterior of a tomato is soft and can bruise easily.
Cut away any rotten or moldy areas on the tomatoes. Use a sharp knife to cut only the affected areas.
Dry the tomatoes thoroughly with a clean towel.