Clinical and virologic manifestations of genital herpes simplex virus type 2 (HSV-2) infection vary widely. We examined frequencies of single-nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs) 2, 3, 4, and 9 in a prospective cohort of 128 HSV-2-infected persons whose viral shedding and lesion frequency was measured by daily sampling from genital secretions. Two TLR2 haplotypes (2 and 4) were associated with increased lesional (P = .008 and P = .03) and shedding (P = .02 and P = .001) rates. An SNP in haplotype 2(-15607A/G) was also associated with shedding (P = .01) and lesional (P = .008) rates. Polymorphisms in TLR2 may be in part responsible for differences in the severity of HSV2 infection.