Cilia, hair-like structures extending from the cell membrane, perform diverse biological functions. Primary (genetic) defects in the structure and function of sensory and motile cilia result in multiple ciliopathies. The most prominent genetic abnormality involving motile cilia (and the respiratory tract) is primary ciliary dyskinesia (PCD). PCD is a rare, usually autosomal recessive, genetically heterogeneous disorder characterized by sino-pulmonary disease, laterality defects, and male infertility. Ciliary ultrastructural defects are identified in approximately 90% of PCD patients and involve the outer dynein arms, inner dynein arms, or both. Diagnosing PCD is challenging and requires a compatible clinical phenotype together with tests such as ciliary ultrastructural analysis, immunofluorescent staining, ciliary beat assessment, and/or nasal nitric oxide measurements. Recent mutational analysis demonstrated that 38% of PCD patients carry mutations of the dynein genes DNAI1 and DNAH5. Increased understanding of the pathogenesis will aid in better diagnosis and treatment of PCD.