Altered commensal microbiota composition has been associated with pediatric type 1 diabetes mellitus (T1D) and inflammatory bowel diseases (IBD), but the causal relationship is still unclear. To search for potential pre-diagnostic biomarkers for pediatric T1D or IBD, we compared microbiota in saliva samples in a nested case-control design comprising children developing T1D (nchildren= 52) or IBD (nchildren= 21) and controls with a similar age, sex, and residential area (nchildren= 79). The pre-diagnostic saliva microbiota alpha- and beta-diversity of children who would develop T1D (nsamples= 27) or IBD (nsamples= 14) minimally varied from that of controls. The relative abundances ofAbiotrophiawere higher, while those ofVeillonella,Actinomyces,Megasphaera,Butyrivibrio, andCandidatus ancillulawere lower in children who would develop T1D. Within 2 years before diagnosis, the metabolic PWY-5677 pathway (converting succinate into butyrate) was lower in pre-T1D samples than in controls (q= 0.034). No significant pre-IBD differences were found. In conclusion, saliva microbiota diversity or composition were not successful predictors for pediatric T1D nor IBD. Intriguingly, the succinate fermentation pathway was predicted to be lowered before the onset of T1D. Thus, investigating functional pathways might provide a better approach in searching for biomarkers for autoimmune disease in the future.