BACKGROUND The microsomal triglyceride transfer protein plays an important role in the folding, assembling and secretion of lipoproteins that contain apoprotein B. Different polymorphisms in the MTTP gene have been associated with risk factors for coronary heart disease and diabetes, the first and fourth most common causes of death in Mexico, respectively. OBJECTIVE The objective of this study was to assess allele, genotype and haplotype frequencies of six MTTP polymorphisms in an unselected Mexican population. METHODS Six polymorphisms were analysed by DNA sequencing of polymerase chain reaction products in 155 Mexican individuals and Hardy-Weinberg equilibrium, genetic variability, linkage disequilibrium and neutrality test were evaluated. RESULTS The rare alleles of the six polymorphisms analysed had frequencies greater than 1% and their genotype distributions were in accordance with Hardy-Weinberg equilibrium. All three promoter and I/T 128 polymorphisms were in linkage disequilibrium. Twelve different haplotypes were observed; GATGGT (70.44%) and TTCGGC (13.91%) were the most common. Diversity patterns in this Mexican population deviate significantly from expectations of the standard neutral model for infinite allele. CONCLUSIONS The -493 G/T, -400 A/T, -164 T/C and I/T 128 polymorphisms can be useful for association studies in this population.