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Primary ciliary dyskinesia (PCD) implies cilia with dysmotility or total absence of motility, which may result in sinusitis, chronicbronchitis, bronchiectasis and male infertility. A large number of deficiencies detectable on the ultrastructural level give rise to PCD, but patients with normal cilia ultrastructure are common. An early diagnosis is very important since PCD can cause permanent lung damage. Diagnosis can be difficult and is based on an abnormal ciliary beat frequency (CBF) and beat pattern, accompanied by specific abnormalities of the ciliary axoneme or normal ultrastructural cilia. In this paper, we present a method to determine CBF through the analysis of phase-contrast microscopy imaging acquired using digital high speed video techniques. Beat frequency measurements are made estimating cilia motion by means of an optical flow algorithm. A previous coregistration process is performed to eliminate cell movements due to cilia motion. The algorithm is tested on several isolated ciliar cells, concluding that this method is a robust technique to determine CBF.