In collaboration with the Slovak Technical University in Bratislava we are developing a programme for automatic quantification of cilia on transmission electron microscopy images. The programme, usually refered to by its working title PCD Quant, has a potential to help in the diagnosis of a rare disease called primary ciliary dyskinesia (PCD). In this disease, cilia move weakly or incorrectly and thus fail to clear the patient's airways. One of the most important diagnostic methods is to examine the structure and number of cilia by electron microscopy. The program should allow for computational processing of TEM images and subsequent determination of the number of cilia recorded and recognition of structural abnormalities. The rapid and accurate evaluation of these data will contribute to improving the diagnostics of PCD.