We present the case of a patient with primary ciliary dyskinesia who later developed clinically probable multiple system atrophy. Multiple system atrophy is a sporadic neurodegenerative disorder clinically characterised by various combinations of parkinsonism, cerebellar ataxia, autonomic failure, and pyramidal sign. Primary ciliary dyskinesia is a genetically heterogeneous disorder of motile cilia and results in chronic bronchitis, bronchiectasis, chronic rhinosinusitis, chronic otitis media, situs inversus, and male infertility. Most of the causative genes for primary ciliary dyskinesia encode proteins that are part of the heavy or intermediate chain of axonemal dynein in ciliary outer dynein arms. We hypothesised that axonemal dynein dysfunction in primary ciliary dyskinesia results in reduced autophagy, accompanied by impaired cytoplasmic dynein function, which in turn accelerates -synucleinopathy in multiple system atrophy. Furthermore, we contemplated a potential association between primary cilia and neuronal function. Although it is not yet clear if a causal link between multiple system atrophy and primary ciliary dyskinesia exists, further investigation into the relationship between axonemal dynein dysfunction in primary ciliary dyskinesia and α-synucleinopathy should be conducted.