The petrotympanic fissure (PTF) and foramen of Huschke (FH) are anatomical structures in the temporal bone that can connect the temporomandibular joint (TMJ) and the ear. The purpose of this retrospective study was to investigate the association between PTF morphology and otalgia and tinnitus, as well as the prevalence of the FH and otological symptoms, using cone beam computed tomography (CBCT). CBCT images from 114 patients presenting with symptoms of a temporomandibular disorder were examined retrospectively. The PTF was classified into three subtypes (open, semi-open, closed) and the presence of the FH was identified. Symptoms of otalgia and tinnitus were obtained from the patient files. The FH was observed in 12.3% of patients examined, and in 12.0% of those with otalgia and 18.9% of those with tinnitus. There was no significant association between the PTF subtypes or the presence of the FH and otalgia or tinnitus (all P > 0.05). The PTF subtype and presence of the FH alone do not appear to contribute to otalgia or tinnitus in patients with temporomandibular disorders.