Primary ciliary dyskinesia (PCD) is a rare genetic disorder mainly characterized by impaired mucociliary clearance and chronic respiratory symptoms. From a consanguineous family, a male patient, although with respiratory complaints since birth, was diagnosed with PCD only in adulthood. Whole-exome sequencing disclosed a novel homozygous intronic single-nucleotide deletion, NM_001369.3(DNAH5):c.13723+4del, initially classified as of uncertain clinical significance. Digital highspeed videomicroscopy (HSVM) evidenced a null ciliary beating frequency; transmission electron microscopy showed absence of outer dynein arms (class-1); and immunofluorescence (IF) demonstrated markedly absent DNAH5 protein level in the apical cilia region with delocalization to the transition and basal-body regions. Bioinformatic analysis predicted altered splicing at the donor splice site of exon 78, whereas mRNA sequencing revealed two splicing defects: the mainly expressed transcript corresponding to exon 78 skipping and a minor transcript originated from a cryptic splice site in exon 78. The patient was infertile and showed severe oligoteratozoospermia. Sperm IF analysis revealed absence of DNAH5 from the flagellum with accumulation at the neck region. The family study confirmed homozygosity. The present results support a pathogenic role for the c.13723+4del variant and underscore the importance of integrating clinical, ultrastructural, DNA, mRNA and protein analyses to clarify and contribute to PCD diagnosis.