<jats:title>ABSTRACT</jats:title><jats:p>This study aimed to investigate the salivary microbiota and metabolome of 13 children with celiac disease (CD) under a gluten-free diet (treated celiac disease [T-CD]). The same number of healthy children (HC) was used as controls. The salivary microbiota was analyzed by an integrated approach using culture-dependent and -independent methods. Metabolome analysis was carried out by gas chromatography-mass spectrometry–solid-phase microextraction. Compared to HC, the number of some cultivable bacterial groups (e.g., total anaerobes) significantly (<jats:italic>P</jats:italic>< 0.05) differed in the saliva samples of the T-CD children. As shown by community-level catabolic profiles, the highest Shannon's diversity and substrate richness were found in HC. Pyrosequencing data showed the highest richness estimator and diversity index values for HC. Levels of<jats:named-content content-type="genus-species">Lachnospiraceae</jats:named-content>,<jats:named-content content-type="genus-species">Gemellaceae</jats:named-content>, and<jats:named-content content-type="genus-species">Streptococcus sanguinis</jats:named-content>were highest for the T-CD children.<jats:named-content content-type="genus-species">Streptococcus thermophilus</jats:named-content>levels were markedly decreased in T-CD children. The saliva of T-CD children showed the largest amount of<jats:named-content content-type="genus-species">Bacteroidetes</jats:named-content>(e.g.,<jats:named-content content-type="genus-species">Porphyromonas</jats:named-content>sp.,<jats:named-content content-type="genus-species">Porphyromonas endodontalis</jats:named-content>, and<jats:named-content content-type="genus-species">Prevotella nanceiensis</jats:named-content>), together with the smallest amount of<jats:named-content content-type="genus-species">Actinobacteria</jats:named-content>. T-CD children were also characterized by decreased levels of some<jats:named-content content-type="genus-species">Actinomyces</jats:named-content>species,<jats:named-content content-type="genus-species">Atopobium</jats:named-content>species, and<jats:named-content content-type="genus-species">Corynebacterium durum</jats:named-content>.<jats:named-content content-type="genus-species">Rothia mucilaginosa</jats:named-content>was the only<jats:named-content content-type="genus-species">Actinobacteria</jats:named-content>species found at the highest level in T-CD children. As shown by multivariate statistical analyses, the levels of organic volatile compounds markedly differentiated T-CD children. Some compounds (e.g., ethyl-acetate, nonanal, and 2-hexanone) were found to be associated with T-CD children. Correlations (false discovery rate [FDR], <0.05) were found between the relative abundances of bacteria and some volatile organic compounds (VOCs). The findings of this study indicated that CD is associated with oral dysbiosis that could affect the oral metabolome.