It has been suggested that apo A-IV may play a role in modulating the activation of lipoprotein lipase (LPL) by apo C-II (Goldberg et al., 1990). Therefore, the role of genetic variation at the apolipoprotein A-IV locus in familial combined hyperlipidemia (FCHL) was investigated. A subset of FCHL patients with half the level of plasma LPL activity was screened by single-strand conformation polymorphism (SSCP) for variants in the apolipoprotein A-IV gene. Two of 20 such individuals were found to be heterozygous carriers of previously undescribed amino acid substitutions: S158L and R 244Q substitutions, designated A-IV-Seattle-1 and A-IV-Seattle-2, respectively. These substitutions were not detected among 20 other FCHL patients with normal LPL levels and among 97 unselected medical students. The finding of these two alleles among only the 20 patients with FCHL with reduced levels of LPL suggests an association with this phenotype. It is hypothesized that these two alleles may contribute, along with alleles of other genes or environmental factors, to the development of FCHL. A third previously undescribed variant (A141S) was observed in four (two homozygotes and two heterozygotes) of the 97 medical students.