Several restriction fragment length polymorphisms (RFLPs) have been identified within or adjacent to the gene locus for apolipoprotein B (apo B), the major protein component of serum low density lipoprotein (LDL). One of these, detected with the restriction enzyme XbaI, has been suggested to be involved in the determination of serum lipid levels in some but not all populations. We determined the XbaI genotypes and serum lipoprotein levels of 176 apparently healthy unrelated Finns. Subjects homozygous (genotype X2X2) or heterozygous (genotype X1X2) for the presence of the XbaI restriction site within the apolipoprotein B gene (n = 113) had, on the average, an 11% higher serum total cholesterol (P = 0.01) level than those homozygous for the absence of this site (genotype X1X1, n = 63). In addition, the X2 allele was significantly associated with apo B(c), another allele reportedly associated with elevated serum cholesterol levels. The combined genotype (both X2 and apo B(c) alleles present) resulted in a greater elevation of total cholesterol (P = 0.004, when compared to subjects with neither allele) and LDL-cholesterol (P = 0.02) than the presence of either allele alone. The results suggest that both the XbaI and apo B(c/g) sites are in linkage disequilibrium with a functionally important DNA alteration within or adjacent to the apo B gene but the XbaI locus may be in stronger linkage disequilibrium.(ABSTRACT TRUNCATED AT 250 WORDS)