Regular bad breath, or halitosis, is caused by bacteria inside your mouth. Most of the odors caused by these bacteria disappear for a time when you brush and floss. However, if you have periodontal disease, the bacteria can live in the deep spaces (pockets) between the gum tissue and tooth, where neither the toothbrush nor the floss is able to reach. This means that no amount of brushing can rid you entirely of your problem.
Periodontal disease is not the only thing that can cause bad breath. Smoking is one of the worst sources of halitosis because the nicotine coats your teeth, tongue, cheeks, and gums, providing an additional surface for the bacteria to adhere to. There are also some medications that can cause your saliva to dry out. Without saliva to flush your mouth, the bacteria can hang around more, and in turn cause you to have bad breath.