Alopecia Areata (AA) is an autoimmune disease characterized by well-circumscribed patches of hair loss especially from the scalp. Cytotoxic T-lymphocyte antigen 4 (CTLA4) gene, a negative regulator of T cells, has been associated with predisposition to most autoimmune disorders. We evaluated two CTLA4 functional single-nucleotide polymorphisms (SNPs) for potential association with Alopecia Areata in an Italian population using a case-control approach. We genotyped +49AG (rs231775) and CT60 (rs3087243) variants in 130 AA patients and 189 ethnically matched controls by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. CTLA4 +49AG analysis revealed no statistically significant difference in both the allele and genotype frequencies between patients and controls. As regarding CT60 SNP, we found that AA cases less frequently than healthy subjects carried A/A genotype with a higher prevalence of A/G and G/G genotypes (83.8 and 75.1 %; p = 0.041, OR = 0.58, 95 % CI 0.32-1.03), consistent with a dominant effect of G disease risk allele. In particular, it seemed to exert effects mainly in DQ7-negative patients with a less aggressive form of the disease. Haplotype analysis suggested that the G(+49AG), A(CT60) allelic combination was significantly related to a reduced disease risk (p = 0.014, OR = 0.28, 95 % 0.09-0.82). Altogether, our findings confirm that only CTLA4 CT60 polymorphism seems to be an important genetic determinant of Alopecia Areata development in Italian subjects.