Lactose persistence (LP) is a genetically determined phenotypic trait, generally related to pastoralism and milk consumption. However, Lactose non-persistence (LNP) results from the progressive decline of Lactase-phlorizin hydrolase (LPH) activity in enterocytes. The Single Nucleotide Polymorphism (SNPs) associated with occurrence of LP/LNP are different for European, Asian, African-American, Northern African and Arab populations. In this study, we studied, the association of these SNPs with LNP in Pakistani patients. Our analysis has evaluated the association between the development of LNP trait and two common variants in intron 13 and 9 (13910-C/T and 22018-G/A) along with the P-value significance level. Therefore in this study, we aimed to access genetic predisposition and clinical manifestations of LNP and LP in 80 subjects (30 subjects with LP and 50 LNP). The presence of T-13910, C-13913, G-13915, G-13907, C-3712, C-13779, A-13937, G-14009, C-14010, T-14011, T-14044, T-14091, A-14107, C-14176, A-14156 and A-22018 polymorphic variants in MCM6-gene were also accessed as reported in different populations. Genomic DNA was extracted from peripheral blood. Consequently, SNPs were analyzed with the PCR-sequencing method. The statistical analysis was performed in SPSS using the method of chi-square test. All the SNPs were evaluated for the association of polymorphism. In the current study 20 out of 30 LP subjects were presented with the following SNPs: C/T-13910 (intron 13) and G/A-22018 (intron 9), representing a frequency level of 0.67 for association. Similar to this frequency of 0.22 and 0.44 was also found in LNP patients. All the SNPs were heterozygous in LP subjects, and for the particular SNP: G/A-22018 (intron 9) 22% heterozygosity was also shown in LNP subjects. This is the first report of SNP in MCM-6 gene studied in Pakistani patients. It may help in better understanding of different diseases having underlying cause related to lactose intolerance.