Background. – The frequency of haplotypes of Nsp I–Eco47 III sites, at the IDUA (α-L iduronidase) gene, in Huichol, Tarahumara and Mestizo Mexican population is reported. Methods. – Eco47 III and Nsp I intragenic polymorphisms in IDUA gene are studied in three (Mestizo, Huichol and Tarahumara populations) Mexican groups. Data from normal Australian [Hum. Genet. 90 (1992) 327] individuals were considered for comparative analyses. Results. – The genotypes for IDUA Eco47 III and Nsp I sites in Mexicans were in agreement with Hardy–Weinberg equilibrium. Allele frequency distributions for individual sites differed (P < 0.05) except at site B1 in the Huichol group. Haplotype Eco47 III–Nsp I frequency distributions were different in the three Mexican normal groups, and it was also observed when to compared with the normal Australians. Conclusions. – This characteristic makes the two IDUA polymorphic sites useful for identification purposes, and these polymorphisms could be included in a PCR based battery of DNA markers.