The increase of bilateral cochlear implantation (CI) in recent years has made it essential to comprehend the effects of CI on otolith function. This study aimed to investigate the development of gross motor and otolith function in patients with inner ear malformations (IEMs) using vestibular-evoked myogenic potentials (VEMPs).Overall, 78 patients with sensorineural hearing loss (SNHL) (age 5.7 ± 4.1 years) were divided into two groups based on the presence (IEM group, n = 39) or absence (control group, n = 39) of IEMs. VEMP testing was performed both before and 1-3 months after CI, and the evaluation of gross motor development was carried out.The mean ages for achieving head control and independent walking were delayed in the IEM group compared with the control group (p = 0.02). The preoperative cervical VEMP (cVEMP) and ocular VEMP (oVEMP) response rates were higher in the control group (60% and 86.95%) than in the IEM group (57.69% and 74.35%) (p < 0.05). Additionally, abnormal cVEMP was associated with delayed acquisition of independent walking (p = 0.017). Saccular and utricular functions after CI were lost by 40% and 31.75%, respectively, in patients who elicited preoperative VEMPs waveform (n = 25).Among SNHL patients, balance development is more delayed in patients of IEMs than in patients without IEMs. The cVEMP and oVEMP waveforms differed greatly between the two groups. The otolith-vestibular nerve conduction pathway can be affected by CI, potentially leading to otolith function impairment. Therefore, it is essential to assess otolith and balance functions before CI, and this evaluation should be considered an integral part of clinical practice.© 2024 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.