Properdin is a component of the alternative activation pathway of the complement system. Deficiency or dysfunction of the protein is inherited in an X-linked recessive manner. Affected males have an increased risk of developing meningococcal disease. Six multi-generation families with different types of properdin deficiency were analyzed using microsatellite and other polymorphisms on the X chromosome. Based on multipoint data, it was found that the disease gene maps close to DXS255 (Zmax = 13.3 at theta max = 0.00) and DXS426 (Zmax = 12.9 at theta max = 0.00) on the Xp-arm near the centromere. There was no indication of genetic heterogeneity among the six families analyzed. Thus it is now possible to perform accurate DNA-based determination of the inheritance of the mutation in affected families.