Optimizing the interface between biomaterials and dental hard tissues can prevent leakage of bacteria or inflammatory mediators into periapical tissues and thus avoid alveolar bone inflammation. In this study, an analysis system for testing the periodontal-endodontic interface using gas leakage and subsequent mass spectrometry was developed and validated using the roots of 15 single-rooted teeth in four groups: (I) roots without root canal filling, (II) roots with an inserted gutta-percha post without sealer, (III) roots with gutta-percha post and sealer, (IV) roots filled with sealer only, and (V) adhesively covered roots. Helium was used as the test gas, and its leakage rate was found by measuring the rising ion current using mass spectrometry. This system made it possible to differentiate between the leakage rates of tooth specimens with different fillings. Roots without filling showed the highest leakage values (p < 0.05). Specimens with a gutta-percha post without sealer showed statistically significantly higher leakage values than groups with a filling of gutta-percha and sealer or sealer alone (p < 0.05). This study shows that a standardized analysis system can be developed for periodontal-endodontic interfaces to prevent biomaterials and tissue degradation products from affecting the surrounding alveolar bone tissue.