Background FOXP3 and ROR-γ genes are master regulators of the Treg and Th17 diferentiation, respectively. This work was planned to investigate the impact of FOXP3 (rs3761548C/A and rs3761549C/T) and ROR-γ (rs9017A/G & rs9826A/G) gene polymorphism on the vulnerability of pediatric Egyptians to acute lymphoblastic leukemia (ALL). Furthermore, we evaluated the impact of these genetic variations on Treg/Th17-related cytokines. Methods FOXP3 SNPs were genotyped using PCR-based restriction fragment length polymorphism (PCR-RFLP), while ROR-γ SNPs polymorphism were performed by PCR-sequence-specifc primer (PCR-SSP). An Enzyme-linked immunosorbent assay (ELISA) was used to assess the levels of Treg/Th17 associated cytokines on 128 ALL children and 124 healthy donors. Results Compared to controls, patients had a signifcant increase (p<0.01/p<0.05) in FOXP3rs3761548CC genotype and a signifcant decrease (p<0.001/p<0.01) inrs3761548CA genotype. A signifcant elevation (p<0.001/p<0.01) in ROR-γ rs9017AA genotype and a signifcant reduction (p<0.01/p<0.05) in rs9017AG genotype were detected in ALL patients versus controls. An insignifcant change in FOXP3 (rs3761549C/T) and ROR-γ (rs9826A/G) genotypes was demonstrated between both groups. ROR-γ GG and GA haplotypes were signifcantly decreased (p<0.05/p<0.05; p<0.05/p<0.05) in ALL subjects compared to healthy ones. Relapsed patients had a signifcantly higher (p<0.05/P<0.05) frequency of FOXP3 rs3761548CA genotype than non-relapsed subjects. ROR-γ rs9017AG and rs9826GG genotypes might be associated with the increase in IL-23 plasma level. Conclusions Our preliminary data provided evidence for the impact ofFOXP3 (rs3761548C/A) and ROR-γ (rs9017A/G) gene polymorphisms and the occurrence of ALL in Egyptian children. Another large-scale prospective study should be conducted to validate these fndings. Keywords Pediatric ALL · FOXP3 · ROR-γ · SNPs · Cytokines · Treg/Th17 cells