Infertility by sperm immotility may be a consequence of axonemal defects, and it is sometimes associated with respiratory disease as in the primary ciliary dyskinesia. The purpose of this study was to investigate the respiratory epithelium of 13 infertile patients with flagellar ultrastructural anomalies whether they suffered or not from respiratory disease. Only one patient had severe respiratory disease. The beat frequency of nasal cilia (9 to 13 Hz) was considered normal in 11 of the 13 patients. All the cilia were found abnormal in one patient. In 12 of 13 infertile men (92.3%), significant ultrastructural cilia anomalies were found (greater than 7%) even though the men did not suffer from any respiratory disease. Axonemal anomalies were found at both levels either of the same type (four cases) or only partially similar (two cases) or totally different (six cases). The most frequently abnormal substructure of cilia was the central complex (10 of 12) even in cases exhibiting a different abnormal pattern at the flagellar level. Findings are discussed according to those found in animal mutants. Our results suggest that ciliary and flagellar axonemes should be controlled both by common and by different groups of genes.