Introduction High-resolution computed tomography (HRCT) scans of the temporal bone are used to assess the bony erosion of the middle-ear structures whenever cholesteatoma is suspected. Objective To study the differences in HRCT Hounsfield unit (HU) index measurements of middle-ear bony structures between an ears with and without cholesteatoma. Methods A retrospective study of 59 patients who underwent surgery due to unilateral cholesteatoma. The HRCT HU index of the scutum, of three middle-ear ossicles, of the lateral semicircular canal (LSCC), and of the fallopian canal was measured in both ears. A comparison was made between the cholesteatoma and the non-cholesteatomatous ear (control). All measurements were conducted by an otolaryngologist. To assess the interobserver bias, 10% of the samples were randomly and independently assessed by another otolaryngologist and a neuroradiologist who were blinded. Results The average HU index was lower in the ear with cholesteatoma when compared with the non-cholesteatomatous ear. While the differences were statistically significant regarding the measurements of the scutum (516.02 ± 311.693 versus 855.64 ± 389.999; p = 0.001), the malleus (1049.44 ± 481.765 versus 1413.47 ± 313.376; p = 0.01), and the incus (498.03 ± 264.184 versus 714.25 ± 405.631; p = 0.001), the differences in the measurements of the LSCC (1042.34 ± 301.066 versus 1154.53 ± 359.609; p = 0.69) and of the fallopian canal (467.19 ± 221.556 versus 543.51 ± 263.573; p = 0.108) were not significantly different between both groups. The stapes was immeasurable in both groups due to its small size. Conclusion Hounsfield unit index measurements are a useful tool that may aid in the diagnosis of early-stage cholesteatoma.