Helicobacter pylori infection, which causes peptic ulcers and gastric cancer, is considered a possible cause of halitosis. Recently, the oral cavity was identified as a possible H. pylori reservoir, particularly in the presence of periodontal disease, which is a cause of halitosis. The purpose of this study was to evaluate by PCR the prevalence of oral H. pylori in the saliva of subjects complaining of halitosis. Samples were obtained from 326 non-dyspeptic subjects, comprising 251 subjects with actual malodour and 75 subjects without halitosis. DNA was extracted from the samples, and the presence of H. pylori and periodontopathic bacteria including Porphyromonas gingivalis, Treponema denticola and Prevotella intermedia was examined by PCR. H. pylori was detected in 21 (6.4 %) of 326 samples. The methyl mercaptan concentration and periodontal parameters including tooth mobility, periodontal pocket depth (PPD) and occult blood in the saliva were significantly greater in the H. pylori-positive subjects. Each of the periodontopathic bacteria was also detected at a significantly higher frequency in the H. pylori-positive subjects. Among those patients with a PPD of ⋝5 mm and a tongue coating score of ⋜2, no difference was observed in oral malodour levels between the H. pylori-positive and -negative subjects. However, the presence of occult blood in the saliva and the prevalence of Prevotella intermedia were significantly greater in the H. pylori-positive subjects. H. pylori was detected in 16 (15.7 %) of 102 subjects with periodontitis, suggesting that progression of periodontal pocket and inflammation may favour colonization by this species and that H. pylori infection may be indirectly associated with oral pathological halitosis following periodontitis.