Auditory dysfunction is the most prevalent injury associated with blast overpressure exposure (Bop) in Warfighters and civilians, yet little is known about the underlying pathophysiological mechanisms. to gain insights into these injuries, an advanced blast simulator was used to expose rats to Bop and assessments were made to identify structural and molecular changes in the middle/inner ears utilizing otoscopy, RNA sequencing (RNA-seq), and histopathological analysis. Deficits persisting up to 1 month after blast exposure were observed in the distortion product otoacoustic emissions (DPOAEs) and the auditory brainstem responses (ABRs) across the entire range of tested frequencies (4-40 kHz). During the recovery phase at sub-acute time points, low frequency (e.g. 4-8 kHz) hearing improved relatively earlier than for high frequency (e.g. 32-40 kHz). Perforation of tympanic membranes and middle ear hemorrhage were observed at 1 and 7 days, and were restored by day 28 post-blast. A total of 1,158 differentially expressed genes (DEGs) were significantly altered in the cochlea on day 1 (40% up-regulated and 60% down-regulated), whereas only 49 DEGs were identified on day 28 (63% up-regulated and 37% down-regulated). Seven common DEGs were identified at both days 1 and 28 following blast, and are associated with inner ear mechanotransduction, cytoskeletal reorganization, myelin development and axon survival. further studies on altered gene expression in the blast-injured rat cochlea may provide insights into new therapeutic targets and approaches to prevent or treat similar cases of blast-induced auditory damage in human subjects. Blast injuries have become prevalent in active duty military personnel due to increased exposure to improvised explosive devices and other explosives during combat operations 1,2. The ears, eyes, lungs, and other air-filled or fluid-filled hollow organs are particularly sensitive to damage from the overpressure and/or under pressure of blast waves 3,4. Auditory dysfunction, manifesting as hearing deficits and tinnitus, is the most prevalent neurosensory disability as a consequence of blast exposure. These disorders may persist for many years, as evidenced by long-term diagnoses of conductive or sensorineural hearing loss or mixed auditory deficits 5-11. Clinical investigations indicate that blast exposures can damage the tympanic membrane, cartilage, ossicles, and muscles of the middle ear that together facilitate the transmission of sound to the inner ear 12,13. Anatomical examination of inner ears from blast-exposed rodents reveals damage to the outer hair cells and to spiral ganglion neurons 9,14 that accompany possible central processing disorders 15. Defects in auditory function can arise from multiple types and levels of injuries, each with significantly different potential recovery outcomes. Middle ear injuries can often be surgically repaired, but structural damage to the inner ear may have a limited ability to recover, due to death of specific associated neuronal cell types, such as h...