Purpose The purpose of this study was to investigate whether the genetic risk factors of age-related macular degeneration (AMD) are associated with the development of choroidal neovascularization (CNV) in highly myopic eyes of elderly Japanese. Methods Highly myopic elderly Japanese patients with and without CNV were genotyped for three AMD-associated single nucleotide polymorphisms (SNPs), namely rs10490924 (A69S) of ARMS2, rs11200638 of HTRA1, and rs1061170 (Y402H) of complement factor H (CFH), with the TaqMan SNP assay. One hundred and eighty-three unrelated highly myopic (axial lengths 426.00 mm or refractive errors 4À6.0 diopters) Japanese patients with CNV who were X50 years of age (mean age ± standard deviation of 62.7 ± 6.3 years) and 170 highly myopic patients without CNV who were X50 years old (62.3±7.1 years) were studied. The differences in the genotypic distributions for the three SNPs between the two groups were tested with the Trend v 2 test, and logistic regression analyses were performed for age and gender adjustment. Results No significant difference was detected in the distribution of the three SNPs, rs10490924 (P40.1), rs11200638 (P40.1), and rs1061170 (P40.5), between the two groups even after adjustments for age and gender differences. Conclusion The genetic risk factors of AMD related to these SNPs do not contribute significantly to the development of CNV in a highly myopic elderly Japanese population.