Objective: To evaluate the relationship between ciliary ultrastructure/genotype and prevalence of neonatal respiratory distress in primary ciliary dyskinesia (PCD). Study Design: This was a retrospective analysis from a multicenter, prospective study of children and adults with PCD. Participants were classified by ultrastructural defect associated with their diagnostic genetic variants: 1) outer dynein arm defect alone (ODA), 2) outer plus inner dynein arm defect (ODA/IDA), 3) inner dynein arm defect with microtubular disorganization (IDA/MTD), 4) DNAH11 (encodes ODA protein but has normal ultrastructure), and 5) normal/near normal/other. The likelihood of neonatal respiratory distress between ultrastructure groups or genotypes was evaluated by multivariate analysis using logistic regression, controlled for age, gender, race, and variant type. Similar analysis was performed within individual genotypes to assess association of neonatal respiratory distress with the presence of 2 loss-of-function variants. Results: Of the 455 participants analyzed, 305 (67.0%) reported neonatal respiratory distress. The odds ratio for neonatal respiratory distress in the DNAH11 group was significantly lower (OR 0.35, 95% CI 0.16-0.76) compared to neonatal respiratory distress in the ODA group. Within the DNAH5 group, those with 2 loss-of-function variants were more likely to have neonatal respiratory distress compared to those with possible residual function variants (OR 3.06, 95% CI 1.33-7). Conclusion: Neonatal respiratory distress is less common in those with DNAH11 variants, thus a high index of suspicion should remain for PCD in the absence of neonatal respiratory distress.