Objectives: Early pre-clinical inflammatory changes in periodontal and/or periapical lesions, which typically precede bone loss, are challenging to diagnose using ionizing-radiation-based imaging modalities. MRI provides relevant additional diagnostic information of inflammatory processes in soft and hard tissues. The aim of the present study is to undertake a systematic review of the literature on MRI in the diagnosis of periodontal and/or periapical disease. Methods and Materials: The PubMed/MEDLINE and Scopus bibliographic databases were searched (2000–2021) using the search string: (“MRI” or “magnetic resonance imaging”) and (“periodontitis” or “periodontal” or “apical pathology” or “endodontic pathology” or “periapical” or “furcation” or “intrabony”). The search was limited to studies published in English. The studies were assessed independently by three reviewers, focusing on the MRI sequences, imaging modalities (radiographs, cone beam CT (CBCT), and MRI), disease definition, assessed parameters, and outcome measurements. Results: The search strategy yielded 34 studies, from which 13 were included. Overall, the findings of MRI were in agreement with CBCT. The studies showed that MRI provided diagnostic information of the hard and soft tissue components affected by periodontal and/or periapical disease with a fairly high sensitivity and specificity. However, the assessed parameters (e.g. MRI acquisition protocols, and disease definition) differed substantially. Conclusions: The included studies indicate that the use of MRI in the diagnosis of periodontal and/or periapical disease is feasible and promising. More studies are needed to define the accuracy of this non-ionizing-radiation-based diagnostic modality, in the assessment of periodontal and/or periapical lesions.