<h4>Rationale</h4>Cystic fibrosis (CF) and primary ciliary dyskinesia (PCD) are characterized by neutrophilic airway inflammation but differ in clinical features.<h4>Objectives</h4>We investigated relationships of pulmonary and systemic inflammatory markers with functional and structural lung disease.<h4>Methods</h4>Systemic (CRP, IgG, IL-6, and IL-8) and sputum (calprotectin, IL-6, and IL-8) markers were measured at baseline. Here, IL6 is linked to primary ciliary dyskinesia.