Age-related macular degeneration (AMD) is a leading cause of legal blindness among older individuals of industrialized countries. In neovascular AMD, which is an advanced stage of AMD, choroidal neovascularization develops underneath the macula and destroys central vision. Oxidative stress is a hypothesized pathway for the pathophysiology of AMD. CD36 was chosen as a candidate gene for neovascular AMD because the protein plays an important role in this pathway as well as in angiogenesis and in maintaining chorioretinal homeostasis. We tested 19 tag single nucleotide polymorphisms (SNPs) across CD36 for their association with the disease in a Japanese population comprising 109 neovascular AMD subjects and 182 unrelated controls. Five of the 19 SNPs demonstrated a nominally significant association with neovascular AMD (P < 0.05), of which two (rs3173798 and rs3211883) withstood Bonferroni correction for multiple testing (rs3173798, nominal P = 9.96 x 10-4, allele-specific odds ratio = 0.55; rs3211883, nominal P = 2.09 x 10-4, allele-specific odds ratio = 0.50). Population structure analyses excluded stratification artifacts in our study cohort. This study supports the candidacy of CD36 as a novel susceptibility gene for neovascular AMD. Replication of our results in other populations will provide further convincing evidence for the genetic association.