Background: Toll-like receptors (TLRs) are involved in the recognition of conserved microbial structures, leading to activation of an inflammatory response and formation of an adaptive immune response. Methods: Twenty-three polymorphisms in five TLR genes were genotyped in 729 tuberculosis cases and 487 healthy controls in a population-based case-control association study in a South African population. Results: We detected sex-specific associations for TLR8 polymorphisms, with rs3761624 (OR = 1.54, p < 0.001), rs3764879 (OR = 1.41, p = 0.011) and rs3764880 (OR = 1.42, p = 0.011) associated in females and rs3764879 (OR = 0.72, p = 0.013) and rs3764880 (OR = 0.75, p = 0.036) associated in males. Epistatic interactions between the TLR genes were investigated and the TLR1_rs4833095 polymorphism was shown to interact with TLR2_rs3804100 and (GT)_n microsatellite (p = 0.002) and alter susceptibility to TB. We also studied the role of TLRs in disease caused by different Mycobacterium tuberculosis genotypes in 257 tuberculosis cases, and identified associations between specific TLR polymorphisms and disease caused by specific strains. Conclusion: This study provides further evidence that the TLRs play an important role in the outcome of tuberculosis disease, and suggests a partial explanation for the male bias in tuberculosis ratios.