Purpose of this study is to identify selected single nucleotide polymorphisms (SNP) of the PAX6 gene and to assess their correlation with congenital iridofundal colobomas and other congenital ocular anomalies.Material and methods. It was a case-control study done on 45 patients aged from 75 days to 58 years (mean age 29.36 ± 14.4 years) with irido-fundal coloboma and 45 healthy controls aged 35.23 ± 13.92 years. Ocular examination was done by using slit-lamp microscopy inspection, fundoscopy and intraocular pressure measurement. Genotyping was done by using the polymerase chain reaction — restriction fragment length polymorphism (PCR-RFLP) method.Results. Two irido — fundal coloboma patients showed CT (+/-) heterozygous genotype of rs667773 SNP and the rest were wild-type CC (-/-) homozygous genotype. All controls showed CC-/- wild-type homozygous genotype. PAX6 SNP rs3026354 showed CC (-/-) wild-type homozygous genotype condition in all patients. Neither CG (+/-) heterozygous nor homozygous GG (+/+) genotype was reported in patients and controls. SNP rs662702, genotype pattern was CC-/- wild type homozygous in all patients and controls. CC genotype frequency was 95.56 and CT genotype was 4.4% while C allele frequency was 97.78 and T allele frequency was 2.22 % in rs667773 C>T SNP. rs3026354C>G SNP had 100 % CC genotype and C allele frequency in both case and control populations. SNP rs 662702C>T showed 100 % CC genotype and C allele frequency in the case and control respectively.Conclusion. The elevated frequency of the CC genotype with C allele was more common in irido fundal patients. Two heterozygous CT genotype of rs667773C>T SNP were reported in two irido-fundal coloboma patients.