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Bad breath usually starts in the mouth, but in some cases, stomach or digestive problems may contribute. Conditions such as acid reflux (GERD), H. pylori infection, and other gastrointestinal disorders can cause persistent bad breath that doesn't improve with brushing or flossing. If you also experience heartburn, stomach discomfort, or a sour taste, the underlying digestive issue may need treatment. A dental exam can rule out oral causes before further medical evaluation is considered.