Halitosis, defined as an unpleasant oral odor, is a commonly experienced condition with a variety of etiological factors and may cause a significant social or psychological handicap to those suffering from it. In most cases, halitosis originates within the oral cavity itself and patients with periodontal disease often suffer from oral malodor. The most common cause of this disease is related to microbiota which reside on the tongue and in the periodontal pocket. This study was undertaken to examine the effect of full mouth disinfection including tongue scraping on oral malodor in a group of patients with chronic periodontitis. The relationship between halitosis and oral health status was also investigated. The volatile sulfur compounds (VSC) scores were significantly correlated with Plaque Index, Bleeding Index, pocket depth, and tongue coating score. The organoleptic ratings were significantly associated with Plaque Index, Bleeding Index, and tongue coating score. The VSC scores and organoleptic ratings correlated strongly with each other. Full mouth disinfection resulted in a significant reduction in the VSC scores, organoleptic ratings, and self-perception of malodor up to 12 weeks. This study indicates that in patients with chronic periodontitis, a full mouth disinfection including tongue scraping has a significant effect in the treatment of oral malodor.