Chronic sinusitis, otitis media with effusion, and upper respiratory tract infections are commonly found in patients with Down syndrome. These diseases are generally felt to be secondary to depressed immune function and altered craniofacial dimensions. Recently, a cilia ultrastructure abnormality was found in a child with Down syndrome. This study is the first to be carried out to determine if cilia ultrastructure abnormalities are prevalent in the population with Down syndrome. Four of 10 patients had documented cilia abnormalities, but these were present in the background of normal cilia, suggesting that they were the result rather than the cause of chronic sinusitis. Similarly, nasal epithelium metaplasia was detected in 50% of the patients. Chronic sinusitis, otitis media with effusion, and recurrent upper respiratory tract infections in children with Down syndrome cannot generally be attributed to primary cilia ultrastructure abnormalities.