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(1) Background: The link between periodontal disease and rheumatoid arthritis (RA) is now widely reported. Several studies suggest the role of <i>Porphyromonas gingivalis</i> (<i>P. gingivalis</i>) in the pathophysiology of RA and some observations highlight the improvement of the disease activity induced by therapies against <i>P. gingivalis</i>. We have very little data on the prevalence of <i>P. gingivalis</i> carriage in patients with juvenile idiopathic arthritis (JIA) and its possible involvement in the pathophysiology of inflammatory joint diseases in children. (2) Methods: The specific IgG responses against <i>P. gingivalis</i> and <i>Prevotella intermedia</i> (<i>P. intermedia</i>) were determined in a cohort of 101 patients with JIA and 19 patients with other autoimmune diseases (inflammatory bowel disease and type 1 diabetes). (3) Results: Specific anti-<i>P. gingivalis</i> and anti-<i>P. intermedia</i> IgG titers were higher in JIA group than in control groups. These differences were mainly observed in the oligoarthritis group. The same pattern was observed in enthesitis-related arthritis (ERA). (4) Conclusions: Children with oligoarticular and ERA subsets had higher IgG titers to <i>P. gingivalis</i> and <i>P. intermedia</i>. These results suggest involvement of an oral dysbiosis in the occurrence of JIA in these subgroups.