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The presence of SARS-CoV-2 in the middle ear reveals the etiopathogenesis of otitis media in COVID-19, as well as an epidemiological risk during otologic examination and surgical procedures in COVID-19 patients. The study included 8 deceased patients with COVID-19. Tissue samples from the middle ear were subjected to virology, histopathology, scanning (SEM) and transmission (TEM) electron microscopy investigation. Ethmoidal mucosa samples were processed for virology analyses. qPCR resulted positive for 75% of nasal mucosa samples and 50% of middle ear samples. Ct values showed lower viral loads in middle ear samples. A proportion of 66.6% patients with positive results in the nasal mucosa showed positive results in the middle ear, and the subtype analysis of the complete genome sequences indicated B.1.1.7 lineage for all samples. In histopathological and SEM samples, no pathological aspects were identified. TEM revealed on the background of death critical alteration of cellular morphology, suggestive structures resembling SARS-CoV-2, goblet cells and immune cells. SARS-CoV-2 can be present in the middle ear of COVID-19 patients even if there is not clinical evidence of acute otitis media. Otolaryngologists could be particularly exposed to COVID-19 infection.