Mutations on the delta-sarcoglycan gene have been associated with the development of both hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy. Recently, the polymorphism c.-94C>G was associated with HCM in Japanese patients. The aim of our study was to evaluate the frequency of c.-94C>G polymorphism in Mexican-Amerindian and Mexican-Mestizo populations. We analyzed the frequency of this polymorphism in 165 Mexican-Amerindian individuals (23 Triquis, 25 Zapotecos, 24 Mayas, 41 Nahuas, and 52 Mixtecos) and 100 unrelated Mexican-Mestizos. Allele frequencies were similar in all Amerindian groups (0.33 Triquis, 0.54 Zapotecos, 0.54 Mayas, 0.46 Nahuas, and 0.49 Mixtecos). When compared with Mexican-Mestizos, only Triquis were different (p = 0.00742). However, when comparing the total sample of the Amerindian population with the Mestizos, the difference was not significant (p = 0.12225). Allele frequencies of Mexican populations were higher than in Asians and less than African and European populations (p < 0.05). These data show that the distribution of the C allele is higher in Mexican populations studied and consequently it is necessary to define if this may be associated with genetic susceptibility for HCM in the Mexican patients.