TRIM5α is a factor contributing to intracellular defense mechanisms against retrovirus infection. Rhesus and cynomolgus monkey TRIM5αs potently restrict HIV-1, whereas human TRIM5α shows weak effects against HIV-1. We investigated the association between a single nucleotide polymorphism in the TRIM5α linker 2 region (rs11038628), which substituted aspartic acid (D) for glycine (G) at position 249, with susceptibility to HIV-1 infection in Japanese and Indian subjects. rs11038628 is rare in Europeans but common in Asians and Africans. Functional analyses were performed by multiple-round replication and single-round assays, and indicated that the G249D substitution attenuated anti-HIV-1 activity of human TRIM5α. A slight attenuation of anti-HIV-2 activity was also observed in TRIM5α with 249D. The predicted secondary structure of the linker region suggested that the 249D substitution extended the α-helix in the neighboring coiled-coil domain, suggesting that human TRIM5α with 249D may lose the flexibility required for optimal recognition of retroviral capsid protein. We further analyzed the frequency of G249D in Japanese (93 HIV-1-infected subjects and 279 controls) and Indians (227 HIV-1-infected subjects and 280 controls). The frequency of 249D was significantly higher among HIV-1-infected Indian subjects than in ethnicity-matched control subjects [odds ratio (OR)=1.52, p=0.026]. A similar weak tendency was observed in Japanese subjects, but it was not statistically significant (OR=1.19, p=0.302). In conclusion, G249D, a common variant of human TRIM5α in Asians and Africans, is associated with increased susceptibility to HIV-1 infection.