Abstract: Primary ciliary dyskinesia (PCD) is a rare monogenic disorder primarily associated with structural and functional abnormalities of motile cilia. It is typically inherited in an autosomal recessive pattern. The disease affects multiple organs, and the variability in clinical phenotypes, along with genetic heterogeneity significantly complicates its diagnosis. Although the application of clinical exome sequencing has significantly improved the diagnostic rate of PCD, more than 30% of patients are still unable to obtain a definitive diagnosis. This article reviews and discusses the pathogenesis, diagnostic methods, and expanding genetic diagnostic approaches for patients with PCD that are negative for exome sequencing. The aim of this article is to assist clinicians in selecting more advanced emerging genetic testing technologies, with the hope of increasing the positive diagnostic rate of PCD, deepening the understanding of its genetic pathogenesis, and laying a foundation for the practice of gene therapy in the future.