The affected-pedigree-member (APM) method of linkage analysis detects linkage by testing for increased marker similarity between affected individuals in a pedigree. Thus, the APM method poses a ‘one-locus’ question about the inheritance of the marker; it requires and makes no assumptions about the inheritance of the disease. It only requires that one be able to accurately determine who is affected. Since the APM method is model free, it is an important tool in testing for linkage of genetically complex diseases for which it is difficult to determine or define an accurate genetic model. In addition, the APM method may be used as a model-free confirmatory test to complement traditional lod score analyses. The X-linked version of the APM method developed here now permits researchers to apply this method to test for linkage of complex diseases to X-linked mark