Background: Among all the polymorphic markers available to date, a hypervariable region located in the 3' of the human apolipoprotein B gene has been extensively studied in global populations throughout the world. Patients and Methods: Using a polymerase chain reaction-based assay, we investigated the allele and genotype frequency distributions of the alleles (corresponding to repeats of a 30 base-pair core DNA sequence) of this hypervariable region in a group of 367 unrelated nationals (201 males, 166 females) from the United Arab Emirates. Results: We found 18 different alleles, ranging from 21 to 55 repeats, making up 51 genotypes that occurred in Hardy-Weinberg proportions and were associated with a heterozygosity index of 80.9%. The allele frequency distribution was different from that of other populations in that it was trimodal, with peaks at 31, 37 and 47 repeats, with corresponding relative frequencies of 16.1%, 25.1% and 6.0%. A four-allele model, which allowed comparisons with other reports, revealed distribution differences with all other ethnic groups except South Asians and Serbs. Conclusion: This marker is very informative for the Emirati population, and will be very useful for UAE-specific DNA fingerprinting. It will also be a valuable tool for assessing the role of apolipoprotein B in cardiovascular diseases.