Human prion protein (PRNP), a copper binding sialoglycoprotein, is the causative agent for transmissible spongiform encephalopathies (TSEs), a group of neurodegenerative diseases that are generally associated with aggregation of amyloid plaques within the central nervous system disrupting the normal tissue structure (Liberski et al. 2001; Aguzzi et al. 2008). While more than 20 PRNP pathogenic mutations have been reported in patients, polymorphisms in the gene have been suggested to influence the incidence of the diseases with a Met129Val polymorphism (rs1799990) being the most important among them (Soldevila et al. 2006). This particular variant has been found to be associated with different prion related diseases as well as cognitive behaviour and long-term memory. Here, as a part of the effort from Indian Genome Variation Consortium (IGVC), we attempt to establish the baseline allele and genotype frequency of four PRNP SNPs including rs1799990 among 24 ethnic groups representing the Indian population. The allele and genotype frequency of rs1799990 is found to be different among different ethnic groups. This pilot study would serve as a platform for future epidemiologicalworks with respect to PRNP SNPs in India.