The aim of this study was to determine whether peptidyl arginine deiminase (PADI) genes could affect susceptibility to tuberculosis (TB), which can be a presumptive base to explain the increased incidence of TB in patients with rheumatoid arthritis (RA) in Korean. The study population consisted of 47 patients with active TB, 35 patients with nontuberculous mycobacterial disease, 50 RA patients, and 83 healthy controls who had received comprehensive medical testing. Genomic DNA was isolated from peripheral blood mononuclear cells using a standard protocol. All of the patients and healthy controls were genotyped for two nonsynonymous SNPs in PADI4, namely PADI4_89, PADI4_90, and one synonymous SNP in PADI4_104. There was the complete linkage between PADI4_89 and PADI4_90 SNPs. In the allele and haplotype analyses of PADI4_89 and PADI4_104, no significant associations are observed between disease groups and control groups. The frequencies of heterozygote (A/G) for PADI4_89 were significantly lower in patients with active TB than in controls [adjusted odd ratios (OR) = 0.35, p values = 0.020]. When the analysis was conducted by overdominant model, more significant associations are observed (adjusted OR = 0.34, p values = 0.005). We found that heterozygote genotypes for PADI4_89 were protectively associated with susceptibility to TB.