<b><i>Introduction:</i></b> The aim of this study is to evaluate signal alteration in the inner ear using three-dimensional (3D)-constructive interference in steady state (CISS) sequence in patients with Ménière’s disease and labyrinthitis and its correlation with clinical and audiological parameters. <b><i>Methods:</i></b> The medical records of the department of otorhinolaryngology were searched for patients with Ménière’s disease or labyrinthitis who underwent MRI with 3D-CISS sequence. Blinded analysis of these patients and of MRI from control subjects without middle or inner ear symptoms was performed to detect any signal asymmetry of the inner ear structures. The results were correlated with clinical symptoms and results of audiological and vestibular tests. <b><i>Results:</i></b> Fifty-eight patients with definite Ménière’s disease and 5 patients with labyrinthitis as well as 41 control exams were included. A separate analysis was performed for patients with probable Ménière’s disease (<i>n</i> = 68). A total of 172 3D-CISS sequences were analyzed by 2 blinded independent neuroradiologists. A CISS-hypointense signal of the inner ear structures was found in 3 patients with definite Ménière’s disease (5.2%), in 4 patients with probable Ménière’s disease (5.9%), and 2 patients with labyrinthitis (40%). No CISS hypointensity was found in the control group. Although no significant difference in symptoms or audiological test results was found between patients with and without this signal change, the side of hypointensity was frequently correlated with the symptomatic side and with hearing impairment. <b><i>Discussion/Conclusion:</i></b> CISS hypointensity of the inner ear structures was evident in patients with clinical conditions other than vestibular schwannoma – more frequently in labyrinthitis than in Ménière’s disease. This signal alteration was frequently encountered on the same symptomatic side as that of the pathological audiology tests, but it is not a predictor for hearing or vestibular impairment.