Ménière's disease patients experience vestibular disability. When most of medical treatments fail, a chemical labyrinthectomy using aminoglycosides is indicated. However, this process frequently causes hearing damage. Aminoglycosides, interacting with mitochondrial rRNAs, alter mitochondrial protein synthesis and the oxidative phosphorylation system, which provide most of the energy in sensory hair cells. For this reason, we hypothesized that genetic variation in mitochondrial rRNA genes and in two nuclear genes coding for proteins that also modify the susceptibility to aminoglycosides might affect the risk of hearing loss in Ménière's disease patients suffering chemical labyrinthectomy. However, there were no differences in mitochondrial rRNA, TFB1M or MRPS12 genetic variation between those patients that experienced or did not experience hearing loss. This is only a pilot study and larger studies are required to use this therapeutic approach in a rational way and decrease the risk of hearing damage.