Familial hypobetalipoproteinemia (FHBL) is an apparently autosomal dominant disorder of lipid metabolism characterized by less than fifth percentile age- and sex-specific levels of apolipoprotein β (apoβ) and low- density lipoprotein-cholesterol. In a minority of cases, FHBL is due to truncation-producing mutations in the apoβ gene on chromosome 2p23-24. Previously, we reported on a four-generation FHBL kindred in which we had ruled out linkage of the trait to the apoβ gene. To locate other loci containing genes for low apoβ levels in the kindred, a genomewide search was conducted. Regions on 3p21.1-22 with two-point LOD scores >1.5 were identified. Additional markers were typed in the region of these signals. Two-point LOD scores in the region of D3S2407 increased to 3.35 at φ = 0. GENEHUNTER confirmed this finding with an nonparametric multipoint LOD score of 7.5 (P = .0004). Additional model-free analyses were conducted with the square root of the apoβ level as the phenotype. Results from the Loki and SOLAR programs further confirmed linkage of FHBL to 3p21.1-22. Weaker linkage to a region near D19S916 was also indicated by Loki and SOLAR. Thus, a heretofore unidentified genetic susceptibility locus for FHBL may reside on chromosome 3.