Background: Primary ciliary dyskinesia (PCD) is a rare autosomal recessive condition of often chronic respiratory infections in early life. A useful tool for early diagnosis of such ciliary abnormalities is transmission electron microscopy (TEM). This study aimed to use TEM to examine these defects and speculate on a diagnosis.Methods: From 2017 to 2019, all referral patients with suspected PCD symptoms were included in this study. Nasal samples were taken after exclusion of further potential differential diagnosis and prepared for TEM. The final diagnosis was based on the International Consensus Guideline for reporting transmission electron microscopy results in the diagnosis of PCD. A descriptive analysis of demographic and ciliary ultrastructural data was performed by SPSS ver 21.Results: Study population consisted of 37 women and 30 men (mean age=20.34±10.7 years). The clinical presentations were as follows: bronchiectasis: 26 patients (38.8%); sinusitis: 23(34.3%); recurrent respiratory infection: 21 patients (31.3%); auditory symptoms: 5 patients (7.5%); situs inversus: 3 patients (4.4%); productive cough: 2 patients (3%); infertility: 2 patients (3%); polyposis: 1 patient (1.5%). According to TEM analysis, 12 (17%) of patients were PCD, 11 (15.7%) were indicating PCD cases, 26 (37.1%) of them had no criteria of PCD and 18 (25.7%) of cases had normal ciliary ultrastructure. Compound cilia and extra-tubule were reported in 29 (41.4%) and 31(44.3%) of patients, respectively. The outer dynein arm defect was seen in 11(16.4%) cases and the inner dynein arm (IDA) defect was seen in 20 (29.8%) cases. Two patients (3%) had microtubular disorganization.Conclusion: Bronchiectasis and sinusitis were the most common complications. The compound cilia and extra-tubule were the most prevalent TEM finding among all participants. However, the most prevalent hallmark diagnostic defects among PCD patients were ODA and IDA defects among PCD patients. Other diagnostic PCD tests should also be performed in patients in the indicating PCD group, those without PCD criteria, and normal patients with a highly suggestive history. Cell-culture, as well, should confirm IDA defects. This study highlights the fundamental need to consider ciliary defect among probable diagnoses and use TEM as a practical diagnostic tool.