To undertake mutation screening of cytochrome P4501B1 (CYP1B1, OMIM 601771) and myocilin (MYOC, OMIM 601652) genes in Egyptian and Saudi Arabian patients with primary congenital glaucoma (PCG).A clinical and molecular genetic study was performed on 11 Egyptian and Saudi Arabian patients with PCG. Clinical diagnosis was confirmed by slit lamp biomicroscopy, gonioscopy, measurement of intraocular pressure, and corneal diameter. The coding regions of CYP1B1 and MYOC genes were amplified by polymerase chain reaction for all affected subjects. Direct sequence analysis was performed to search for sequence alterations. Haplotype analysis and genotype/phenotype correlation were carried out.Three CYP1B1 mutations were identified in 5 PCG patients (45.4%) of which 2 were novel (homozygous E173K and heterozygous N498D) and the third (G61E) had previously been reported. In addition 10 single nucleotide polymorphisms were identified in CYP1B1 and MYOC genes of which 2 were novel. However, no pathologic changes in either of the genes were detected in the remaining 6 patients.This is the first report of molecular genetic analysis of PCG in the Egyptian population in which 2 novel mutations have been identified. It is possible that these mutations are specific to this population and may lead to alterations in the protein structure encoded by the gene. Patients with no mutations in the screened genes may have mutations in genes yet to be identified.