Abnormal ciliary axonemal structure and function are linked to the growing class of genetic disorders collectively known as ciliopathies, and our understanding of the complex genetics and functional phenotypes of these conditions has rapidly expanded. While progress in genetics and biology has uncovered numerous cilia-related syndromes, primary ciliary dyskinesia (PCD) remains the sole genetic disorder of motile cilia dysfunction. The first disease-causing mutation was described just 13 y ago, and since that time, the pace of gene discovery has quickened. These mutations separate into genes that encode axonemal motor proteins, structural and regulatory elements, and cytoplasmic proteins that are involved in assembly and preassembly of ciliary elements. These findings have yielded novel insights into the processes involved in ciliary assembly, structure, and function, which will allow us to better understand the clinical manifestations of PCD. Moreover, advances in techniques for genetic screening and sequencing are improving diagnostic approaches. In this article, we will describe the structure, function, and emerging genetics of respiratory cilia, review the genotype-phenotype relationships of motor ciliopathies, and explore the implications of recent discoveries for diagnostic testing for PCD.