The distribution of mRNAs coding for three different isoforms of the alpha and two of the beta subunit of Na,K-ATPase was studied in the rat vestibular system using in situ mRNA hybridization. The dark cells of the utricular macula and of the ampullae of the semicircular canals expressed high levels of mRNA encoding the alpha 1 and beta 2 isoforms of the Na,K-ATPase, a composition that in the cochlea has been uniquely found in the stria vascularis. However, in the dark cells it was coupled with a weak expression of beta 1. The sensory epithelia of the vestibular system showed alpha 1 and beta 1 expression at much higher levels than in the cochlear sensory epithelium. Weak expression limited to the alpha 1, beta 1, and beta 2 isoforms was observed in the endolymphatic sac, contrasting previous cytochemical results which suggested extensive Na,K-ATPase activity to the sac. The results support the widely held hypothesis that the vestibular dark cells play a role similar to that of the stria vascularis in endolymph production. They indicate that the ion transport requirements of the vestibular sensory epithelia may be different than those in the cochlea. They also suggest that the endolymphatic sac may not be a major site of inner ear ion exchange.