Purpose: The aim of this study was to examine the effect of chlorhexidine disinfection, as a chemical method of oral hygiene practice, and subsequent use of probiotics on halitosis in children. The effects of mechanical and chemical oral hygiene practice methods on the severity of halitosis were also assessed. Materials and Methods: 208 children with organoleptic test (OLT) scores of 2 or more were randomly assigned to four groups: A: conventional oral hygiene practices (COH) including toothbrushing and flossing; B: COH + tongue scraping (TS); C: COH + TS + chlorhexidine; D: COH + TS + chlorhexidine + probiotics. OLT was performed at 1-week and 3-month follow-ups. Results: A significant and stable number of participants showed major and moderate levels of improvement in OLT scores in group D (p 0.001). The improvement of OLT scores in group C was also significant (p 0.001), but not stable over the follow-ups (p = 0.44). Neither significant nor stable improvements in the OLT scores were detected in groups A and B through follow-ups (p > 0.05). Conclusion: Probiotic therapy following oral disinfection with chlorhexidine may reduce the severity of halitosis over longer periods. Keywords: antimicrobial agent, chlorhexidine, halitosis, oral hygiene, probiotics