The respiratory tract (i.e., airways and alveoli) is in close contact with the milieu that is outside the human body and thus, in addition to its role in exchange of gases, it is needed to protect the human being from outside threats such as microbes and pollution. Respiratory tract diseases can have major detrimental effects on human health with increased risks for morbidity and mortality. An example of this dilemma is the orphan disease, primary ciliary dyskinesia (PCD), a complex genetic disorder linked with myriad genetic mutations involving over 50 genes and over 2000 pathogenic variants that lead to dysfunction of vital human components including the respiratory tract, auditory system, mechanisms of fertility and others. The core defect involves abnormal function and motion of microscopic organelles called cilia found throughout the human body with abnormal mucociliary clearance (i.e., aberrant mucociliary escalator). The regulation of motile cilia that are involved in various aspects of physiology such as respiration and reproduction is via thousands of genes. PCD pathophysiology, genetic underpinnings, diagnosis and principles of treatment are considered in this review of primary ciliary dyskinesia in pediatric persons (i.e., newborns, children and adolescents). Primary ciliary dyskinesia (PCD) is one of many ciliopathies that is identified as a condition with remarkable phenotypic and genetic variability. In this fluid fluctuation phenomenon, some PCD patients exhibit classic features such as chronic respiratory disease, situs abnormalities, and infertility, while others may present with milder or atypical disease. In certain cases, ultrastructural analysis of cilia may appear normal despite underlying dysfunction. Disease severity can range from early-onset bronchiectasis to relatively preserved pulmonary function into adulthood, reflecting perplexing genotype-phenotype diversity. Testing for PCD requires an experienced team with expertise in sophisticated technology that includes nasal nitric oxide (nNO) analysis, transmission electron microscopy (TEM), immunofluorescence analysis (IFA), high-speed video-microscopy analysis (HSVMA), three-dimensional explant spheroid formation (3D-E; ex vivo technique), genetic studies and others. Genetic testing is recommended for those suspected of having PCD, as for example in certain neonates (i.e., persistent respiratory distress, unexplained rhinorrhea with chronic cough, situs inversus), at-risk children (i.e., having persistent wet cough, chronic sinusitis, unexplained bronchiectasis, recurrent otitis media with airway symptomatology) and adults with early childhood respiratory symptoms often associated with infertility. The medical evaluation is complicated by various factors including the absence of a gold standard for a precise diagnosis. Also, as the clinician or clinical team considers a patient with possible PCD, the testing that is done should keep in mind the differential diagnoses of PCD; these conditions include cystic fibrosis (CF), various immune disorders, numerous infections (i.e., tuberculosis, aspergillosis, others), alpha-1-antitrypsin deficiency (AATD) and others as noted in this article. As emerging cutting-edge 21st century research seeks treatment of PCD via gene therapy, current management involves intense therapy of upper and lower respiratory tract infections (i.e., rhinosinusitis, otitis media, pneumonia) as well as bronchiectasis with focused efforts at dealing with impaired mucus clearance. Primary ciliary dyskinesia is a classic example of how microscopic (electron microscopic) maladies can lead to major macroscopic maladies in newborns, children, adolescents and adults.