Background: This study aimed to investigate the distribution of virulence factor genes in Shigella strains isolated from children with diarrhea in the southwest, Iran.Methods: In this cross-sectional study, a total of 91 Shigella spp. were isolated from diarrhea specimens of 1 530 children aged under 15 years in Ahvaz and Abadan, southwest Iran. The Shigella strains were identified by biochemical methods. Subsequently, Shigella spp. were identified by polymerase chain reaction (PCR).All Shigella spp evaluated by PCR for the presence of 9 virulence genes (ipaH, ial, virF, invE, sat, sigA, pic, pet, and sepA).Results: A total of 91 isolates including 47 S. flexneri, 36 S. sonnei, and 8 S. boydii were identified. All isolates were positive for the ipaH gene. The other genes include ial, virF, invE, sigA, sat, sepA, pic and pet found in 84.6%, 72.5%,68.1%, 62.6%, 51.6%, 39.5%, 37.3% and 28.5% of the isolates, respectively.Conclusion: Our results showed a high distribution of virulence genes among Shigella strains in our region. It seems that for different Shigella spp. different virulence factors contribute to pathogenesis. The current study provided insights into some baseline information about the distribution of some virulence genes of Shigella isolates in Southwest Iran.