Toll-like receptors (TLRs) are essential elements of the innate immune response to different infections including the infection with human immunodeficiency virus (HIV). Single nucleotide polymorphisms (SNPs) in TLRs such as TLR4 1063A/G and 1363C/T have been found to be associated with changes in CD4 count, viral load (VL), and disease progression during HIV infection. However, the association of these SNPs with the pathogenesis during HIV infection is controversial. We investigated the frequency of TLR4 1063A/G and 1363C/T SNPs in 168 Omani donors [68 HIV-infected patients (>3% of Omani HIV-infected patients) and 100 healthy controls] and the association of these SNPs with the VL, CD8 and CD4 counts, and the immune recovery after cART as observed by CD4 T cell increase. SNPs were analyzed after the amplification of the regions that contain them by polymerase chain reaction (PCR) and sequencing of the PCR products. The TLR4 1063GG genotype was detected in the HIV-infected group only. No association was found between the studied SNPs and the average VL during 1 year of infection, the average CD4 and CD8 count during 1 year of viremia, the nadir CD4 count, the CD4 count when the patient reached VL < 50 copies/mL due to cART, and the ratio of the CD4 count 3 and 6 months after reaching VL < 50 copies/mL after cART to the last CD4 count before reaching VL < 50 copies/mL. Our study suggests that TLR4 (1063A/G and 1363C/T) SNPs have no association with the VL or the CD4 and CD8 counts during HIV infection.