This study was performed to determine the genetic diversity of HLA class I and II alleles among two ethnic groups in Southeastern Iran. HLA profiles were determined in 71 Iranian populations (41 Zaboli and 30 Baloch). The frequencies of HLA-A02 (p=0.017), -Cw4 (p=0.003), and -DR8 (p=0.025) in the Zaboli populations were significantly higher than that in Baloch ethnic group. In contrast, the frequency of HLA-A23 allele was more frequent in Baloch than Zaboli (p=0.020). This report represents an important resource for investigators in the fields of transplantation immunology and population genetics from widely dispersed areas of Iran.