Microsatellite polymorphisms are widely used to map the genes responsible for inherited disorders. The most commonly used detection is based on radioactive labelling and autoradiography. We now present the successful detection of fluorescence-labelled allelic fragments on an automated DNA sequencer. This allows for safer and quicker detection as well as a potential for more efficient processing of the data, e.g. for linkage analysis. The system was tested in the mapping of properdin deficiency, an X-linked condition with increased risk for a severe infection in the affected.