One third of the world’s population is suspected to be infected with Mycobacterium tuberculosis with an estimation of 8-10 million new cases diagnosed annually. Despite low contribution from the human immunodeficiency virus, Pakistan is among the 22 high tuberculosis (TB) burden countries worldwide. Among the several factors that contribute towards the susceptibility to active tuberculosis, evolution of cytokine and chemokine responses are crucial for the disease progression and establishment. Cytokines modulate the activities of target cells and initiate immune response while chemokines are important in the recruitment of immune cells to the site of infection. Polymorphisms in genes encoding for cytokines and their receptors can have a broad effect on killing mycobacteria, which reside and multiply within the macrophages. The role of interferon gamma (IFN-γ) is to activate macrophages to kill intracellular organisms. Single nucleotide polymorphisms (SNPs) in key cytokine genes may affect the functionality of IFN-γ and may result in high and low producer phenotypes. A number of SNPs have been identified in the IFN-γ and IFN-γ modulating genes that may predispose to mycobacterial diseases. However, the relevance of polymorphisms within these genes to the common phenotype of TB remains unclear. The frequency distributions of cytokine SNPs in various populations have been shown to be highly variable and this may be due to evolutionary pressures in different populations. Therefore, the aim of the current study was to investigate the functional gene polymorphisms in IFN-γ (+874 T→A), IFN-γ receptor 1 (IFN-γR1) (-273 to -741) and in IFN-γ modulating cytokines and chemokines such as interleukin 10 (IL-10) (-1082 A→G), tumor necrosis factor alpha (TNF-α) (-308 G→A), interleukin 6 (IL-6) (-174 G→C) and C-C chemokine ligand 2 (CCL-2) (-2518 A→G) to establish the baseline frequencies and to investigate their influence on TB disease susceptibility and severity in indigenous population. Moreover, chemokine CCL-2 protein levels were also assessed on a subset of samples. When cytokine genotype frequencies were analysed in healthy individuals, Pakistani population seems to have a higher proportion of alleles which were associated with high IFN-γ (T), high IL-10 (A), low TNF-α (G), high IL-6 (G) and low CCL-2 (A) phenotypes as reported from other Asian populations compared to Caucasian and African populations. This underlines the importance of a ‘local’ reference population when evaluating the clinical relevance of cytokine gene polymorphisms. In relation to TB, the IFN-γ T allele was found to be higher in pulmonary TB (PTB) patients which was restricted to pulmonary minimal and moderate TB groups and increases the odds of developing pulmonary TB by 2-3 folds. The TT genotype was also found to be associated with the first intronic CA11 repeats in moderate pulmonary TB group while AA was found to be associated with CA13 repeats in extrapulmonary disseminated TB (DTB) disease. Two novel SNPs in IFN-γR1 promoter region at positions -255 (C→T) and -129 (G→A) were found in association with pulmonary advanced (PAD) and extrapulmonary disseminated TB patients respectively, which suggest the association of these SNPs with TB disease severity. The IFN-γ modulating cytokine SNPs were also found in association with differing susceptibility and severity of TB such as IL-10 SNP (-1082) Ahigh allele with protection in pulmonary advanced and extrapulmonary TB disease, TNF-α SNP (-308) Ahigh allele with susceptibility to extrapulmonary TB disease and IL-6 SNP (-174) Clow allele with protection in pulmonary TB disease. Investigation of CCL-2 genotype-phenotype relation showed that CCL-2 GG genotype and higher CCL-2 levels may play a role in TB disease localization. interactions, the combinations of IFN-γ TT high In terms of mutiloci or IFN-γ AAlow alleles with IL-6 GGhigh allele were the most significant in increasing the odds of developing TB disease severity which is in line with the reported function of IL-6 as a part of the Th2 network. Our results suggest that combinations of key cytokine genotypes provide more meaningful associations of polymorphisms with TB disease susceptibility and severity. This study also provides useful information with respect to genetic biomarkers associated with disease susceptibility and severity in TB. Such information in the future can help National TB control programs for the identification of high risk groups in TB.