Although not all causes of oral malodor are entirely understood, most unpleasant odors are known to arise from proteins trapped in the mouth which are processed by oral bacteria. Over 600 types of bacteria can be found in the average mouth, of which several dozens produce high levels of foul odors when incubated in the laboratory.

The most common location for mouth-related halitosis is the tongue. Large quantities of naturally-occurring bacteria are often found on the posterior dorsum of the tongue, where they are rather undisturbed by normal activity. This part of the tongue is relatively dry and poorly cleansed, and bacterial populations can thrive on remnants of food deposits, dead epithelial cells and postnasal drip (PND). The convoluted microbial structure of the tongue dorsum provides an ideal habitat for anaerobic bacteria, which flourish under a continually-forming tongue coating of food debris, dead cells, postnasal drip and overlying bacteria, living and dead. When left on the tongue, the anaerobic respiration of such bacteria can yield either the putrescent smell of indole, skatole, polyamines, or the "rotten egg" smell of volatile sulfur compounds (VSCs) such as hydrogen sulfide, methyl mercaptan and dimethyl sulfide.

The foul odors are mainly produced due to the anaerobic breakdown of proteins into individual amino acids, followed by the further breakdown of certain amino acids to produce detectable foul gases. For example, the breakdown of cysteine and methionine produce hydrogen sulfide and methyl mercaptan respectively. Volatile sulfur compounds have been shown to be statistically associated with oral malodor levels, and usually decrease following successful treatment.

The nasal passages are known as the second major source of bad breath. In this instance, the odor exiting the nostrils has a pungent odor which differs from the oral odor. Nasal odor may be due to sinus infections or a disturbance to the normal airflow, in cases such as foreign bodies or a deviated septum.

Putrefaction from the tonsils is generally considered a minor cause of bad breath (contributing to some 3-5% of cases). Although some people (approximately 5% of the population) suffer from small bits of calcified matter in tonsillar crypts (called tonsilloliths or “tonsil stones”), which themselves smell extremely foul when released, they do not necessarily cause bad breath. Clinical experience shows that in most cases where malodor origins from the tonsils, the conservative treatment is enough to solve the problem, but in the more severe cases, laser cryptolysis should be considered.

There are a few systemic (non-oral) medical conditions which may cause foul breath odor, but these are extremely infrequent in the general population. Such conditions are:

1. Trimethylaminuria ("fish odor syndrome").
2. Diabetes mellitus.
3. Fetor hepaticus: an example of a rare type of bad breath caused by chronic liver failure.
4. Lower respiratory tract infections (Bronchial and lung infections).
5. Carcinoma.
6. Renal infections and renal failure.
7. Metabolic dysfunction.

Since these conditions are rare, may not display bad breath at all, and will most likely show additional characters (which are more conclusive, diagnostically, than the breath odor), people suffering from halitosis should not immediately conclude that they suffer from these conditions or diseases just by deducing from the oral malodor alone.

Most researchers consider the stomach as a very uncommon source of bad breath (except in belching). The esophagus is a closed and collapsed tube, and continuous flow of gas or putrid substances (as opposed to a simple burp) from the stomach indicates a health problem - such as reflux or a fistula between the stomach and the esophagus - which will demonstrate more serious manifestations than just the foul odor.