The inherited prion diseases are neurodegenerative disorders which are not only genetic but also transmissible. More than a dozen mutations in the prion protein gene that result in nonconservative amino acid substitutions segregate with the inherited prion diseases including familial Creutzfeldt-Jakob disease (CJD). In Israel, the incidence of CJD is about 1 case/10(4) Libyan Jews. A Lys200 substitution segregates with CJD and is reported here to be genetically linked to CJD with a lod score of > 4.8. Some healthy elderly Lys200 carriers > age 65 years were identified, suggesting the possibility of incomplete penetrance. In contrast, no linkage was found between the development of familial CJD and a polymorphism encoding either Met129 or Val129. All Libyan Jewish CJD patients with the Lys200 mutation encode a Met129 on the mutant allele. Homozygosity for Met129 did not correlate with age at disease onset or the duration of illness. The frequency of the Met129 allele was higher in the affected pedigrees than in a control population of Libyan Jews. The frequency of the Met129 and Val129 alleles in the control Libyan population was similar to that found in the general Caucasian population. The identification of three Libyan Jews homozygous for the Lys200 mutation suggests frequent intrafamilial marriages, a custom documented by genealogical investigations.