Purpose: Osteoarthritis (OA) is also known as degenerative arthritis and it affects millions of people and can have a huge impact on their lives. Single Nucleotide Polymorphisms (SNPs) in combination with genome wide association studies (GWAS) have been significantly focused. GWAS have been evaluated using candidate genes with genetic variants for Growth Differentiation Factor 5 (GDF5), Component of Oligomeric Golgi complex 5 (COG5), and Cytochrome B-245 alpha chain (CYBA) with primary knee Osteoarthritis (OA). These studies have been documented in Caucasian population, and we aimed to investigate the case-control study to evaluate association between knee OA in the South Indian population. Materials & methods: SNPs for GDF5 (rs143383), COG5 (rs4730250) and CYBA (rs4676) were genotyped with polymerase chain reaction and restriction fragment length polymorphism in 150 primary Knee OA cases and 150 age and gender-matched controls. Alleles and genotype frequencies were calculated to compare the significant and non-significant association with the p-values. Multifactor dimensionality reduction (MDR) analysis was performed to study the gene-gene and gene-environment interactions. Results: Baseline clinical details such as Body Mass Index (BMI), weight, histories of Type 2 diabetes and hypertension were significantly associated with primary Knee OA (p<0.05). Genetic factors for 3 SNPs were significantly associated with allelic frequency, dominant, and recessive mode of inheritance pattern (p<0.05). MDR analysis revealed a strong synergistic interaction between GDF5 and CYBA as well as COG5 and CYBA gene polymorphisms. GDF5 gene polymorphism is also synergistically interacting with BMI. Conclusion: The three gene polymorphisms of GDF5, COG5 and CYBA could be used as a molecular biomarker to identify primary Knee OA in south Indian population to assess the risk of disease which in turn helps us to reduce the disability caused by the disease. To the best of our knowledge this is the first study in India.