primary ciliary dyskinesia (pcD) is a genetically heterogeneous syndrome that results from defects in motile cilia. The ciliary axoneme has a 9 + 2 microtubule structure consisting of nine peripheral doublets surrounding a central pair apparatus (CPA), which plays a critical role in regulating proper ciliary function. We have previously shown that mouse models with mutations in cpA genes CFAP221, CFAP54, and SPEF2 have a PCD phenotype with defects in ciliary motility. In this study, we investigated potential genetic interaction between these cpA genes by generating each combination of double heterozygous and double homozygous mutants. no detectable cilia-related phenotypes were observed in double heterozygotes, but all three double homozygous mutant lines exhibit early mortality and typically develop severe PCD-associated phenotypes of hydrocephalus, mucociliary clearance defects in the upper airway, and abnormal spermatogenesis. Double homozygous cilia are generally intact and display a normal morphology and distribution. Spermiogenesis is aborted in double homozygotes, with an absence of mature flagella on elongating spermatids and epididymal sperm. These findings identify genetic interactions between CPA genes and genetic mechanisms regulating the cpA and motile cilia function. Primary ciliary dyskinesia (PCD) is a syndrome resulting from dysfunction of motile ciliary clearance in the respiratory system, the brain, the fallopian tube, and the embryonic node, as well as sperm flagellar motility 1-5. It is genetically heterogeneous and commonly inherited in an autosomal recessive manner, although mutations causing X-linked recessive and autosomal dominant inheritance have been reported 6-9. Approximately 1 in 16,000 children are affected and typically exhibit chronic upper and lower airway infection, otitis media, male infertility, and situs inversus. Neonatal respiratory distress, congenital heart defects, female infertility, and hydrocephalus are also associated at a lower frequency. The core, or axoneme, of the motile cilium has a 9 + 2 microtubule structure with nine doublets along the outer periphery surrounding a central pair apparatus (CPA) 4,10. Ciliary motility is generated by dynein arms associated with the outer microtubule doublets and is regulated by the CPA, radial spokes connecting the outer and central microtubules, and the dynein regulatory complex. The cilia on the embryonic node possess a 9 + 0 microtubule structure without a CPA. A substantial number of mouse models of PCD has helped uncover the role of novel genes in ciliary function and PCD pathogenesis 4,5. However, only a few studies have investigated epistatic interaction of these genes. Mice lacking dynein assembly factor coiled coil domain containing protein 40 (CCDC40) have situs inversus with randomized expression of left-right patterning marker NODAL during gastrulation 11,12. Homozygous mutants that are also heterozygous for a NODAL mutation fail to establish left isomerism or left-sided expression of NODAL 12 , demonstrating that ...