Mental retardation (MR) is a condition in which a person having an intelligence quotient (IQ) lowers than 70. It is also associated with a deficit in adaptive behavior such as communication and daily living skills. Mental retardation is either non-syndromic or syndromic. It is one of the most common genetic disorders and it affects about 1-3% of the human population, with a ratio of males higher than females. The present study was can-ied out to determine the prevalence of families having mental retardation in Pakistani population. In the present study, 7 MR families with three or more affected individuals with MR were enrolled. Family history was taken and pedigree was made personally by visiting the families. The blood samples were collected from the enrolled families. Then DNA was extracted from the blood samples collected from these families by standard inorganic protocol. After isolation of DNA from blood samples, 3 STR markers (D4S191, D4S2392 and D4S3024) in vicinity of mental retardation (MR) locus (MRT1)/gene PRSS12 were amplified on each sample of each family by PCR. The amplified PCR product was first checked on agarose gel and then genotyping analysis (linkage analysis) was performed on non denaturing polyacrylamide gel (PAGE). After polyacrylamide gel electrophoresis, picture of the gel was taken and alleles were read manually with larger allele donated by 2 and smaller by 1. After that haplotype was constructed to determined the pattern of inheritance among the affected and normal individuals of each family under study and also to determined that a family was linked or unlinked to mental retardation locus (MRTI)/gene PRSS12. None of the family was linked to mental retardation locus/gene PRSS12. The families which remain unlinked to the reported loci during screening signifies extreme genetic heterogeneity of MR which is not surprising because about 50% of human protein coding genes are expressed in the brain and it provides an excellent resource material for mapping of the new genes which will shed light on the complex pathways involved in the development of learning and memory in those population. The pedigree of each family in the present study showed that most of the marriages are cousin marriages; therefore this study may play a role in creating awareness about the effect of cousin marriages that is the first step towards decreasing socio-economic burden of the country by genetic counseling and also to prevent mental retardation in Pakistan due to inbreeding. Mental retardation locus (MRT1)/gene PRSS12 was studied for linkage analysis in seven families from different areas of District Swat and Peshawar of Khyber Pakhtunkhwa province of Pakistan. None Out of seven families was linked to mental retardation locus (MRT1 )/gene PRSS 12. All the seven families remain unlinked to this locus. It is concluded that Mental retardation is a complex genetic disorder and needs further studies to identify the already known locus or to explore novel loci through genome wide scan responsible for mental retardation in these population. This will provide opportunities of genetic counseling to these populations and will ultimately result in prevention of mental retardation in Pakistani population.