Primary open angle glaucoma (POAG) is the most common type of glaucoma. Among the POAG genes identified so far, myocilin (MYOC) is the most frequently mutated gene in POAG patients worldwide. The MYOC Gln48His mutation is unique among Indian POAG patients. This mutation has not been observed in some populations within India and in other populations worldwide. The objectives of this work were to characterize and compare the mutation spectrum among POAG patients from two places of South India and identify the occurrence and prevalence of Gln48His mutation in our study populations.One hundred-one (101) POAG patients from Chennai, South India were recruited for the study. Earlier, 100 patients from the southernmost part of India, Kanyakumari district, were screened. MYOC was screened by polymerase chain reaction based single stand conformation polymorphism (PCR-SSCP) methodology. DNA sequencing of deviant samples was performed. Secondary structures of the proteins with amino acid sequence variations were predicted.The mutation frequency of MYOC among POAG patients in Chennai was 2%. Three types of mutations were observed. The MYOC Gln48His mutation was observed among 2 POAG patients from Chennai. However, absence of this mutation among patients from Kanyakumari suggests possible involvement of demographic factors in disease causation via this mutation. Two heterozygous sequence variants, Thr353Ile and Asn480Lys, in the same exon (exon III) of MYOC were observed in one POAG patient who had a severe disease phenotype. This is the first such report of a compound heterozygote individual with two mutations in the same exon of MYOC.The presence of mutations at a rate similar to other studies suggests the causative role of MYOC among POAG patients from Chennai. Screening of more patients and families from all parts of India is required to identify the actual frequency of the Gln48His mutation and thus highlight its importance. The compound heterozygote with a severe disease phenotype reiterates the importance of MYOC in certain POAG patients.