Background and aim Hashimoto's thyroiditis (HT) pathogenesis is characterized by a dysregulation of immune tolerance, which may be influenced by genetic variations in the FOXP3 gene, a key regulator of T-regulatory cell function. However, the role of specific FOXP3 polymorphisms in HT susceptibility is not yet fully understood, particularly in Middle Eastern populations. This study aims to explore the association between the FOXP3 rs2232368 polymorphism and HT susceptibility in an Iraqi population while also examining its relationship with thyroid function parameters. Methods This case-control study included 60 HT patients and 40 healthy controls from the Medical City Educational Laboratories in Baghdad (October 2022 to September 2023). HT diagnosis was based on established clinical and laboratory criteria. Thyroid function (thyroid-stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4)) was measured using the mini VIDAS