To detect and evaluate early signs of apical periodontitis using MRI based on a 3D short-tau-inversion-recovery (STIR) sequence compared to conventional panoramic radiography (OPT) and periapical radiographs in patients with apical periodontitis. Patients with clinical evidence of periodontal disease were enrolled prospectively and received OPT as well as MRI of the viscerocranium including a 3D-STIR sequence. The MRI sequences were assessed for the occurrence and extent of bone changes associated with apical periodontitis including bone edema, periradicular cysts, and dental granulomas. OPTs and intraoral periapical radiographs, if available, were assessed for corresponding periapical radiolucencies using the periapical index (PAI). In total, 232 teeth of 37 patients (mean age 62±13.9 years, 18 women) were assessed. In 69 cases reactive bone edema was detected on MRI with corresponding radiolucency according to OPT. In 105 cases edema was detected without corresponding radiolucency on OPT. The overall extent of edema measured on MRI was significantly larger compared to the radiolucency on OPT (mean: STIR 2.4±1.4 mm, dental radiograph 1.3±1.2 mm, OPT 0.8±1.1 mm, P=0.01). The overall PAI score was significantly higher on MRI compared to OPT (mean PAI: STIR 1.9±0.7, dental radiograph 1.3±0.5, OPT 1.2±0.7, P=0.02). Early detection and assessment of bone changes of apical periodontitis using MRI was feasible while the extent of bone edema measured on MRI exceeded the radiolucencies measured on OPT. In clinical routine, dental MRI might be useful for early detection and assessment of apical periodontitis before irreversible bone loss is detected on conventional panoramic and intraoral periapical radiographs.