Abstract Introduction Hashimoto thyroiditis (HT) is a hypothyroid disease disorder and is one of the most prevalent type of autoimmune thyroid disease (AITD) that occur in humans. The human cytotoxic T lymphocyte antigen 4 (CTLA- 4) gene encodes a T-cell surface molecule critical for controlling T-cell tolerance. Several polymorphic forms of this gene have been detected in HT. One of the HT polymorphisms is a nucleotide replacement of adenine by guanine at position 49 (A49G) of exon 1 and several studies have shown a strong correlation between Hashimoto’s disease and this CTLA-4 gene polymorphism in other populations but not in the Lebanese population. Objectives To determine the correlation between gene polymorphism of A49G in exon 1 of CTLA-4 gene and Hashimoto thyroiditis in the Lebanese population. Materials and Methods A number of 98 Lebanese subjects (56 Hashimoto patients and 42 control subjects) were recruited. Genomic DNA was isolated from whole blood and amplified by Polymerase Chain Reaction followed by Restriction Fragment Length Polymerase. The products’ genotypes were then identified by agarose gel electrophoresis. The effects of this polymorphism were investigated on T3, T4, TSH, TPOAb, TgAb, vitamin D and age at onset of the disease in HT patients. ix Results The wild type AA genotype was found in 23 (41.1%) of patients, AG genotype in 23 (41.1%) and GG genotype in 10 (17.9%). Statistical analysis showed a trend toward greater A49G SNP in patients with GG genotype compared with the wild type AA genotype, although this association did not quite reach statistical significance (P-value=0.073). Statistical analysis showed significance in AG and GG genotypes as compared to wild type genotype AA in TSH (P-value=0.043) but not in T3, T4, TPOAb, TgAb, vitamin D and age at onset of the disease. Conclusion Our results showed an increase in GG genotype in patients compared to the WT AA genotype in controls although this did not quite reach statistical significance (P-value = 0.073)