The aim of this study was to determine the genetic variations associated with the mannose-binding lectin 2 (MBL2) gene in rheumatic heart disease (RHD) patients in the Vellore region, South India. This study included 50 patients with RHD and equal number of age and sex matched healthy controls. The genomic DNA was extracted from peripheral blood, to find out the genetic variations if any in MBL2 gene. The exon 1 of MBL2 gene was amplified by polymerase chain reaction (PCR) and then screened with Single Strand Conformation Polymorphism (SSCP) analysis. DNA sequencing was carried out in ABI PRISM® 3730 DNA analyzer. The sequence data were edited as required using the sequence analysing software and sequences were aligned using Autoassembler version 2.0 software. Four novel mutations in four RHD patients in exon 1 of MBL2 gene were observed, (1) 46 G/A (Heteroplasmic mutation) (2) 47 G (deletion), 3) 67 G → A (serine to phenyl alanine) and (4) 96 G (insertion). This is the first report of these novel mutations detected in exon 1 of MBL2 gene of RHD patients in South India. The clinical importance of the study is understanding the genomic nature of every population may show variation in its degree of susceptibility to any environmental insults. ©2010 Academic Journals.