Background: The FOXP3 gene provides instructions for producing the forkhead box P3 (FOXP3) protein. The FOXP3 protein attaches (binds) to specific regions of DNA and helps control the activity of genes that are involved in regulating the immune system. Aim: This study intended to analyze SNPs in FOXP3 gene in the coding region, 5`UTR and 3`UTR using bioinformatics tools and visualizing the 3D structure of the gene. Methods: SNPs were retrieved from NCBI, and the protein sequences were retrieved from UniprotKB. SIFT and Provean software was used to predict whether the nsSNPs were tolerated or deleterious. Polyphen- 2 for nsSNPs function prediction on the produced protein.I-mutant and Mupro software to check the protein stability, finally PHD software to see whether the nsSNPs were related to a disease or not.Regulomedb to predict the regulatory element for 5`UTR region. For the 3`UTR PolymiRTs database to predict the variation in microRNA (miRNA). FuncPred software to show the unknown function for the selected SNPs.TheI-TASSER to visualize the 3D structure. Results: A total of 205 SNPs were retrieved, 180 SNPs in the CDS region, 20 in 3`UTR, 5in 5`UTR. SIFT prediction resulted in 93 deleterious and 87 toleratednsSNPs, Proveanrevealed60 deleterious and 120 tolerated,Polyphen-2 resulted in 29 probably damaging,11 possiblydamaging, 3 benign and 2 no result. I-mutant showed 12nsSNPs increasing, and 25 decreasing the protein stability, MUpro resulted in 3nsSNPs increasing the protein stability and 42 decreasing the protein stability, PHD resulted in 17 nsSNPs as disease related and 28 as neutral. For noncoding SNPs, Regulomedb resulted in 11 SNPs, PolymiRTs result in 11, and FuncPred result. Conclusion: The analysis of FOXP3 gene showed that from 205 nsSNPs only 11 SNPs are highly damaging and 20 SNPs found in the 3UTR region which predicts its function using different methods. Still bioinformatics software have their limitations, the results from this study may be convenient in future for further population based research activities and towards development of perfect medicines.