To assess the reliability of judging the spatial relation between the inferior alveolar nerve (IAN) and mandibular third molar (MTM) based on MRI or CT/CBCT images. Altogether, CT/CBCT and MRI images of 87 MTMs were examined twice by 3 examiners with different degrees of experience. The course of the IAN in relation to the MTM, the presence/absence of a direct contact between IAN and MTM, and the presence of accessory IAN were determined. The IAN was in > 40% of the cases judged as inferior, while an interradicular position was diagnosed in < 5% of the cases. The overall agreement was good (κ = 0.72) and any disagreement between the imaging modalities was primarily among the adjacent regions, i.e., buccal/lingual/interradicular vs. inferior. CT/CBCT judgements presented a very good agreement for the inter- and intrarater comparison (κ > 0.80), while MRI judgements showed a slightly lower, but good agreement (κ = 0.74). A direct contact between IAN and MTM was diagnosed in about 65%, but in almost 20% a disagreement between the judgements based on MRI and CT/CBCT was present resulting in a moderate overall agreement (κ = 0.60). The agreement between the judgements based on MRI and CT/CBCT appeared independent of the examiner's experience and accessory IAN were described in 10 cases in MRI compared to 3 cases in CT/CBCT images. A good inter- and intrarater agreement has been observed for the assessment of the spatial relation between the IAN and MTM based on MRI images. Further, MRI images might provide advantages in the detection of accessory IAN compared to CT/CBCT. MRI appears as viable alternative to CT/CBCT for preoperative assessment of the IAN in relation to the MTM.