Among the seven investigated FCN1 SNPs, all of which occur within a TAD, the combination of the most 5′ five alleles (AAAGDelT), present in the *3B2, *3C1, *3C2, and *3C2.3A haplotypes, occurred with higher frequency among blood donors than among HBV+ leprosy patients (OR = 0.6 [95%CI = 0.39–0.9], P = 0.014). This evidence concerns the gene FCN1 and leprosy.