Oral malodor affects a large proportion of the population and may be the cause of a significant social and psychological handicap. This pilot study aimed to examine whether a 1-stage full-mouth disinfection in periodontitis patients (scaling and root planing of all pockets within 24 hours together with the application of chlorhexidine to all intra-oral niches followed by chlorhexidine mouth rinsing for 2 months) resulted in a significant improvement in malodor when compared to a fractionated periodontal therapy (consecutive root planings per quadrant, at a 1 to 2 week interval). The baseline and outcome data concerning oral malodor were linked to the presence of tongue coating and to its roughness (fissures). Twenty-four patients with severe periodontitis were randomly allocated to test and control groups. At baseline and after 1 and 2 months, the concentration of volatile sulfur compounds (VSC) in the mouth was measured and organoleptic ratings (expired air and total mouth air) were given. Plaque samples were collected from the dorsum of the tongue to calculate the number of colony forming units (CFU) per ml (anaerobic culturing) as well as the number of pigmented CFU/ml. Both the baseline organoleptic ratings and the VSC scores correlated well with the presence of tongue coating but not with the tongue roughness. Because a correlation between tongue coating and its microbial load could not be detected, it was hypothesized that the tongue coating per se, and not the bacteria, might be responsible for the malodor. The 1-stage full-mouth disinfection resulted in a faster and additional reduction in the organoleptic ratings of the oral malodor, even after 2 months. This might be explained by the improved periodontal outcome and/or the more significant reduction in the CFU/ml of pigmented species. In contrast to the organoleptic ratings, which were significantly reduced in both treatment groups (when compared to baseline), the VSC levels remained unchanged. This pilot study indicates that a 1-stage full-mouth disinfection has, in comparison to a standard periodontal therapy, additional beneficial effects in the treatment of oral malodor.