Vitamin D receptor (VDR) gene variants are associated with differential susceptibility or resistance to tuberculosis in different ethnic groups. We investigated the polymorphisms in the 5′ regulatory region of VDR gene in 206 normal healthy subjects and 166 patients with pulmonary tuberculosis from south India. Cdx-2 polymorphism was studied by polymerase chain reaction (PCR) with allele-specific primers, while genotyping of A1012G was done by PCR-based restriction fragment length polymorphism. A significantly decreased frequency of Cdx-2 G allele (P = 0.016) and G/G genotype (P = 0.010) and an increased frequency of A-A haplotype (A allele of Cdx-2 and A allele of A1012G) (P = 0.015) were observed in patients compared to controls. The study suggests that Cdx-2 G/G genotype may be associated with protection and A-A haplotype with susceptibility to tuberculosis.