Axonemes are organelles that are composed of microtubule doublets and singlets with a complex assembly of associated proteins. This study was designed to investigate the possibility that an abnormal axoneme is involved in the pathogenesis of Usher's syndrome. A masked structural and functional analysis of sperm was performed on samples from ten patients with Usher's syndrome and 33 controls, including duplicate samples from six patients and three controls. In the functional analyses, there was a significant decrease in patient sperm motility and velocity. Structurally, there was a significant increase in tail abnormalities at both the light and electron microscopic levels. Ejaculate volume and sperm concentration were normal in the patient population. The presence of abnormal axonemes was also confirmed in remnant photoreceptors of a whole eye donation from a patient with Usher's syndrome. The data suggest that defective connecting cilia axonemes may be involved in the irreversible, progressive loss of photoreceptors in Usher's syndrome.