SummaryThe genetic relationship amongst apolipoprotein B (apo B) gene polymorphisms (signal peptide insertion/deletion (Leu‐Ala‐Leu‐16/‐14),XbaI (Thr2488),EcoRI (Glu4154→ Lys), Asn4311→ Ser, 3′ ‐VNTR) has been investigated in samples of South Asian (Indian) and Swedish individuals. The frequency distribution of alleles at all these sites was found to be significantly different between the South Asian and the Swedish samples (deletion allele: 0·20v.0·31, X + (presence ofXbaI cutting site): 0·29v.0·55, R‐ (absence ofEcoRI cutting site): 0·11v.0·19, Ser4311: 0·45v.0·19). The distribution of allele frequencies at the VNTR site was bimodal in both populations. However, in South Asians, the most common allele was a 35 repeat unit allele, whilst in the Swedish sample, and in all other reports from Caucasian samples the 37 repeat unit allele was the most frequent (South Asianv.Swedish: 35 allele: 0·36v.0·19, 37 allele: 0·25v.0·48). Furthermore, four new alleles at the apo B gene 3′ ‐VNTR site (15, 17, 32, 38 repeat unit alleles) were observed in South Asians, of which two (15 and 17 repeat unit alleles) were well outside the bimodal distribution. In both samples, strong linkage disequilibrium and allelic association were detected between alleles at the 3′ ‐VNTR and each of the other sites, and also between theins/delandXbaI sites and between theXbaI and Asn4311→ Ser sites. The same five common haplotypes as defined byins/del, XbaI,EcoRI and Asn4311→ Ser were found to be present in both samples comprising 97 and 99 % of the haplotypes observed in the South Asian and Swedish samples respectively. Detailed analysis revealed the predominant occurrence of certain 3′ ‐VNTR alleles on specific haplotypes and demonstrates the usefulness of the VNTR site for haplotyping and representative association studies. A model for the evolutionary relationship of the major haplotypes including the 3′ ‐VNTR site is presented. These findings support a mechanism of replication slippage as a major factor for the generation of new alleles at the apo B