Our aim was to ascertain whether fatty liver may be present in the genetic form of familial hypobetalipoproteinemia (FHBL) linked to a susceptibility locus on chromosome 3p21. Three genetic forms of FHBL exist: (a) FHBL caused by truncation-specifying mutations of apolipoprotein B (apoB), (b) FHBL linked to chr3p21, and (c) FHBL not linked either to APOB or to chr3p21. Fatty liver is common in apoB-defective FHBL. Hepatic fat contents were quantified by magnetic resonance spectroscopy in 16 subjects with 3p21-linked FHBL, 32 subjects with apoB-defective FHBL, and 39 sex- and age-matched controls. Mean liver fat of 3p21 subjects was similar to controls and approximately 60% lower than apoB-defective FHBL subjects ( P = .0012). Indices of adiposity (body mass index, waist/hip ratio) and masses of abdominal subcutaneous, retroperitoneal, and intraperitoneal adipose tissue (IPAT) were quantified by MR imaging. Mean measures of adiposity were similar in the 3 groups, suggesting that adiposity per se was not responsible for differences in liver fat. Liver fat content was positively correlated with IPAT. The intercepts of regression lines of IPAT on liver fat content were similar in controls and 3p21, but higher in apoB-defective FHBL subjects. The slopes of the lines were steepest in apoB-defective, intermediate in 3p21, and flattest in controls. Lipoprotein profiles and very low density lipoprotein-apoB100 kinetics of 3p21 and apoB-defective groups also differed. Thus, 2 genetic subtypes of FHBL also differ in several phenotypic features.