Familial combined hyperlipidemia (FCHL) was originally described as a disorder characterized by elevated levels of either plasma cholesterol or triglyceride (TG) or both in members ofthe same family. More recent studies have indicated that apolipoprotein B levels (apoB) are also elevated in these individuals. Although a dominant mode of inheritance was originally proposed, recent studies have questioned this simple mode of inheritance, and the genetic basis of the disorder has eluded investigators. A study that reported evidence that FCHL is linked to the apolipoprotein AI-CIII-AIV region on chromosome 11 is therefore of interest. We have attempted to replicate this finding in three large, well-characterized FCHL kindreds by using a highly polymorphic marker in the apoCIII gene. Using the same definitions and parameters as were used in the initial report, we obtained strong evidence against linkage of FCHL to the apolipoprotein AI-CIII-AIV region on chromosome 11 (combined lod score of -7.87 at 0% recombination). Two other models, one based on total cholesterol (TC) levels alone and one based on the joint distribution of TC and apoB levels, also gave evidence against linkage of FCHL to this region (lod scores at 0% recombination of -8.95 and -2.58, respectively). An additional regression-based linkage analysis also gave no support for the existence of a locus in this region that influences these lipid levels in these pedigrees. Explanations for the differences in results between these studies include genetic heterogeneity, differences in clinical phenotype used to select the pedigrees, and ascertainment bias.