Purpose The PAX6 gene is a homeobox gene involved in oculogenesis, ocular growth, and form-deprivation myopia. Our aim was to determine whether PAX6 polymorphism at position À12 of intron 9 (IVS9-12C to T, rs667773) is associated with high myopia in Chinese Taiwanese. Methods This case-control study compared a study group (n ¼ 188) with high myopia whose spherical equivalent was greater than À6.0 D with a control group (n ¼ 85) whose spherical equivalent was less than À0.5 D. Genotyping of IVS9-12C to T was conducted by restriction fragment length polymorphism analysis, and results were compared for the two groups. Results No significant difference in genotype and allelic frequency at this position between the study and control groups was detected. However, there was a significantly higher frequency of the CC genotype in extremely myopic (greater than À10 D) patients (Po0.001, odds ratio (OR ¼ 5.265), confidence interval (CI ¼ 2.0342-13.626)). Furthermore, there was a higher frequency of the C allele in the extreme myopia group than in the control group (P ¼ 0.002, OR ¼ 3.73, CI ¼ 1.57-8.81). Conclusions The elevated frequency of the CC genotype within the extreme myopia group indicated that the CC genotype could act as a genetic marker, identifying patients predisposed to develop extreme myopia. Varied expression of this genotype may contribute to the genetic predisposition to high myopia in Chinese Taiwanese.