The measurement of hydrogen-methane breath gases is widely used in gastroenterology to evaluate malabsorption syndromes and bacterial overgrowth. Laboratories offering breath testing provide variable guidance regarding oral hygiene practices prior to testing. Given that oral dysbiosis has the potential to cause changes in breath gases, it raises concerns that oral hygiene is not a standard inclusion in current breath testing guidelines. The aim of this study was to determine how a pre-test mouthwash may impact hydrogen-methane breath test results. Participants presenting for breath testing who had elevated baseline gases were given a chlorhexidine mouthwash. If a substantial reduction in expired hydrogen or methane occurred after the mouthwash, breath samples were collected before and after a mouthwash at all breath sample collection points for the duration of testing. Data were evaluated to determine how the mouthwash might influence test results and diagnostic status. In 388 consecutive hydrogen-methane breath tests, modifiable elevations occurred in 24.7%. Administration of a chlorhexidine mouthwash resulted in significantly (p ≤ 0.05) reduced breath hydrogen in 67% and/or methane gas in 93% of those consenting to inclusion. In some cases, this modified the diagnosis. Mean total gas concentrations pre-and post-mouthwash were 221.0 ppm and 152.1 ppm (p < 0.0001) for hydrogen, and 368.9 ppm and 249.8 ppm (p < 0.0001) for methane. Data suggest that a single mouthwash at baseline has a high probability of returning a false positive diagnosis. Variations in gas production due to oral hygiene practices has significant impacts on test interpretation and the subsequent diagnosis. The role of oral dysbiosis in causing gastrointestinal symptoms also demands exploration as it may be an underlying factor in the presenting condition that was the basis for the referral.Hydrogen-methane breath testing is a widely used diagnostic tool, based on the science that these gases are byproducts of saccharide fermentation by gut microorganisms, rather than human metabolism.Glucose, lactose, and fructose are normally absorbed in the small intestine. Increased gas production following their ingestion is associated with malabsorption or premature fermentation due to excessive bacteria in the small intestine. Hydrogen and methane gas are absorbed from the gastrointestinal tract, exhaled via the lungs and are thus measurable in breath. Increased gas production following ingestion of fructose or lactose are used to detect malabsorption of carbohydrates. Similarly, increases in expired breath gases in response to ingestion of non-digestible lactulose, or glucose are used to predict small intestinal bacterial overgrowth (SIBO) [1][2][3][4] .In-depth discussion on the methodology and interpretation of breath testing was published in 2009 5 and a shorter summary in 2011 6 . The concept that expired breath gases may be influenced by the oral microbiome is not yet an integrated component of breath testing guidelines, even though oral dysbiosis h...