Objective: To investigate the clinical manifestations, diagnosis and treatment processes of two siblings with PCD caused by the same compound heterozygous mutations in DNAAF2. Methods: With clinical diagnosis of PCD, the two siblings were recruited in the study. We collected their clinical histories, laboratory tests, bronchoscopy, otoscope images, and radiographic data. Whole blood of the siblings and their parents were separately harvested for whole-exome sequencing and Sanger sequencing. Results: The 7-year-old girl presented with recurrent respiratory tract infection, sinusitis and otitis media. Auxiliary examinations showed pneumonia, atelectasis, bronchiectasis, low nitric oxide concentration (nNO), and conducting hearing loss. The younger brother, 10-month boy, exhibited pneumonia, sinusitis, otitis media, intestine malrotation and with lower nNO, atelectasis in chest CT, obstructive ventilator dysfunction by pulmonary function and conductive hearing loss. Two compound heterozygous mutations in DNAAF2 were detected in both of the siblings, nonsense mutation c.156C＞A and frameshift mutation c.177_178insA, and the c.177_178insA (p.E60Rfs*3) mutation is a novel mutation. Conclusion: The study enriches our knowledge of clinical manifestations and genetic information of PCD caused by DNAAF2.