The ultrastructural analysis of cilia and diagnosis of primary ciliary dyskinesia (PCD) in biopsies of airway epithelium is sometimes confounded by poor sampling, inconsistencies in tissue quality and processing, and other technical problems. Although clinical findings may lead to a presumptive diagnosis, ultrastructural analysis of ciliary axonemes is the standard for confirmation of PCD. The ultrastructural features of the cilium when viewed in cross section by transmission electron microscopy confer a radial symmetry to the axoneme. Current digital image processing techniques can be applied to such images to reinforce signal, diminish noise, and confirm consistency of position of axonemal structures, a process that can augment ultrastructural analysis for PCD. In this study, computer-assisted digital image processing was used to evaluate cross sections of cilia in airway epithelial biopsies from patients previously diagnosed with PCD as well as in control subjects with normal cilia. These studies supported the original diagnoses and provided some new insights into axonemal organization in PCD. This technique is simple and may be useful in providing a supporting means for confirming or ruling out a diagnosis of PCD in cases that appear equivocal.