Background: Myopia has raised a predominant public concern among minors. A recent genome-wide association study (GWAS) identified six novel loci in Asian adults. Whether these genetic loci works for myopia in minors remains unknown and worthy of exploration. Methods: In order to validate the findings, here we performed a case-control study (600 myopia minors, 110 high myopia (HM) minors, and 800 non-myopia minors as controls) utilizing the TaqMan single nucleotide polymorphism (SNP) genotyping assays. Adjusted odds ratios (ORs) and 95% confidence intervals (CIs) was adopted. Results: The median ages in controls, myopia, and HM were 15.1, 15.0, and 15.1, respectively, while the means +/- standard deviations for them were 0.32 +/- 0.41, - 3.2 +/- 1.6, and -9.8 +/- 2.2, respectively. We found rs2246661 (allelic OR: 1.29; 95% CI: 1.09-1.52; P =0.003), rs74633073 (allelic OR: 1.41; 95% CI: 1.12-1.78; P =0.004), and rs76903431 (allelic OR: 1.42; 95% CI: 1.11-1.81; P =0.005) were significantly associated with increased risk of myopia. Rs2246661 was also significantly associated with increased risk of HM in minors (OR: 1.37; 95% CI: 1.02-1.84; P =0.035). Conclusion: We identified three loci contributed to myopia in minors and these findings gave new insight into the genetic susceptibility mechanisms of myopia at the molecular level.