Knowledge of the facial nerve anatomy during otological surgery is crucial in avoiding an iatrogenic injury to the facial nerve. In this study, the authors investigated the anatomical relationship between the tympanic portion of the facial canal (FC) and the mastoid portion of the facial nerve using multi-slice computed tomography (CT). The authors reviewed multi-slice CT scans of 364 ears in 351 patients. They categorised the facial nerve anatomy into three subgroups based on the course of its mastoid portion relative to the tympanic portion of the FC: lateral running course (LRC); on the tympanic line course (OL); and medial running course (MRC). They also compared the proportions of these anatomical courses between ears with middle ear inflammation (MEI) and without middle ear inflammation (non-MEI). The 364 ears were divided into 281 with MEI and 83 in the non-MEI group. Among the 364 ears, 15% were categorised as LRC, 30% were OL and 55% were MRC. The proportion of LRC ears in the MEI group (17%) was significantly higher than that in the non-MEI group (7%) (p<0.05). Although there was a tendency for the facial nerve to run more laterally in ears with MEI than in non-MEI ears, measured by the mean distance between the tympanic FC and most lateral part of MP on axial CT, the difference was not statistically significant. This study concludes that the MP of the facial nerve has various courses relative to the tympanic portion and there is an increased likelihood of LRC facial nerve in MEI. Otologists, particularly less experienced surgical trainees, should be aware of this and carefully evaluate the course of the facial nerve on multi-slice CT so that they are less likely to cause an inadvertent iatrogenic injury of the facial nerve.