BACKGROUND/AIMS Kostmann syndrome, or severe congenital neutropenia, is an autosomal recessive disease of neutrophil production and is associated with severe periodontal pathology. The aim of this study was to determine whether human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV) contribute to the pathogenesis of Kostmann syndrome periodontitis. METHODS Supragingival plaque and saliva samples were taken from a 6-year-old boy and his 3-year-old sister suffering from Kostmann syndrome, and from two age- and gender-matched healthy children serving as controls. The samples were taken before and 24 months after periodontal treatment. Real-time polymerase chain reaction (TaqMan Real-Time PCR) assay was used to quantify HCMV and EBV DNA. RESULTS EBV was detected in baseline samples from the Kostmann syndrome patients but not in samples from the healthy control subjects. HCMV was only detected in the saliva of the boy with Kostman syndrome at baseline. Herpesviruses numbers decreased dramatically in the post-treatment samples. CONCLUSION EBV and HCMV were detected in the two subjects with Kostmann syndrome periodontitis. The results of the study indicate that nonsurgical treatment of Kostmann syndrome periodontitis can reduce supragingival and salivary herpes viral loads.