The metabolic syndrome is characterized by the clustering of several traits, including obesity, hypertension, decreased levels of HDL cholesterol, and increased levels of glucose and triglycerides. Because these traits cluster, there are likely common genetic factors involved. We used a multivariate structural equation model (SEM) approach to scan the genome for loci involved in the metabolic syndrome. We found moderate evidence for linkage on chromosomes 2, 3, 11, 13, and 15, and these loci appear to have different relative effects on the component traits of the metabolic syndrome. Our results suggest that the metabolic syndrome components, diabetes, obesity, and hypertension, are under the pleiotropic control of several loci.