The gold standard for the diagnosis of primary ciliary dyskinesia (PCD) is a dynein deficiency shown with transmission electron microscopy. However, there are many cases of PCD without dynein deficiency. When considering ciliary function, there are similar problems of sensitivity in diagnosis and there is also a major lack of specificity. Based on the normal ciliary function and ultrastructure and the absence of secondary abnormalities after ciliogenesis in sequential monolayer-suspension culture, the diagnostic value of ciliary function analysis after ciliogenesis was investigated in more than 70 PCD and 640 non-PCD cases. In biopsies, ciliary immotility was found in 66% of PCD cases but was also found in 8% of non-PCD cases. PCD was later confirmed in 61% of the biopsies with ciliary immotility. Normal ciliary beat frequency (CBF) was found in 20% of PCD biopsies. Coordinated ciliary activity was observed in 10% of PCD cases. After ciliogenesis in culture, ciliary immotility was present in 78% of the PCD cases but never in non-PCD cases. CBF was normal after ciliogenesis in 7% of the PCD cases and was always found in non-PCD cases. Absence of coordinated ciliary activity was found in 100% of PCD cases and 0% of non-PCD cases. In conclusion, while ciliary function analysis in a biopsy never proves, nor excludes the diagnosis of PCD, after ciliogenesis in culture CBF measurement can be diagnostic for PCD and reaches 100% specificity and sensitivity when considering coordinated ciliary activity, making it the single 100% diagnostic parameter for PCD.