Dinucleotide polymorphisms are short tandem repeat sequences that can be used as probes for haplotype analysis in Duchenne's muscular dystrophy (DMD). There are approximately a total of 50,000 to 100,000 such loci in the human genome, and they are highly informative due to the variability of allele lengths at these loci. Primers can be designed to amplify across such repeats located in the dystrophin gene to provide diagnostic information when RFLP analysis is uninformative. We report the usefulness of three such loci for analysis of DMD families in Singapore. The STR50 marker consists of (CA)n repeats located in intron 50 of the dystrophin gene while DYS1 marker is located upstream to the transcriptional start site for the brain dystrophin promoter and BSTRH marker is identified in the 3' untranslated region of the gene. End-labeled PCR products were resolved on 6% denaturing polyacrylamide sequencing gel. Alleles were identified by comparison with sequencing markers. PCR product typically ranged between 174 bp to 255 bp with five to six alleles observed. The heterozygosity rates estimated from 50 X chromosomes of unrelated individuals were 76.0% (BSTRH), 86.6% (DYS1) and 93.3% (STR50). In 38 DMD families studied, the results obtained show that these markers were highly informative and reveal Mendelian mode of inheritance. They were useful for linkage analysis, identification of deletion mutations, confirmation of paternity and mapping of gene recombination.