BACKGROUND Primary ciliary dyskinesia (PCD) is a rare genetic disease associated with abnormalities in the structure and function of cilia. The common clinical presentation of PCD is characterized by otitis media, chronic rhinosinusitis (CRS), chronic bronchitis, and infertility due to impaired ciliary motility. PCD is a complex disease and its diagnosis is complicated. However, there are some clinical features that are strong indicators of PCD, namely situs inversus, chronic otitis media, CRS, and chronic bronchitis with wet cough. CASE REPORT A 49-year-old male who had already received 3 operations for refractory CRS presented with nasal discharge, post nasal discharge, and chronic wet cough. Since childhood, he had suffered from otitis media, rhinosinusitis, and bronchitis. He also had a family history of CRS. He was diagnosed as having male infertility at another hospital, but the details were unknown. We performed a fourth surgery and obtained the nasal mucosa for electron microscope analysis during the operation. The transmission electron microscopic findings of the nasal cilia revealed several abnormalities in structure including a central complex defect, microtubular disorganization, and an inner dynein arm defect. Based on these findings and clinical courses, we made the definitive diagnosis of PCD. CONCLUSIONS When faced with refractory CRS cases with characteristic clinical symptoms that are associated with otitis media, chronic bronchitis, and infertility, clinicians should consider the possibility of PCD.