Objective: Diabetes Mellitus has been a prevailing chronic disease in the Philippines with prevalence rate of 5.5% in men and 6.1% in women according to WHO in 2016. Type 2 Diabetes Mellitus (T2DM) is characterized as the inability of the pancreatic β-cells to compensate with higher demanded insulin. This study aims to determine the feasibility of using Single Nucleotide Polymorphism (SNP) variants of the three genes: KCNQ1 rs2237895, TCF7L2 rs7903146 and DPP4 rs4664443 as prognostic biomarkers of T2DM by SNP correlation in genetically predisposed Filipinos. Methods: DNA samples were gathered from 7 normoglycemic and 7 diabetic participants from Ospital ng Tondo, Manila. Primers were designed using primerBLAST based on target genes verified using the BLASTn suite. Amplification conditions were optimized with annealing temperatures 60.2°C for KCNQ1, 54.8°C for TCF7L2 and 56.5°C for DPP4 in accordance to the designed primers. Product visualization was performed through Agarose Gel Electrophoresis and were sent to the Philippine Genome Center for sequence verification. Polymerase Chain Reaction - Restriction Fragment Length Polymorphism (PCR-RFLP) genotyping was performed using restriction enzymes SmaI for KCNQ1 and RsaI for TCF7L2 and DPP4, which cleaves target products with minor allele variants of each respective SNP. Results: In KCNQ1, incidence of homozygous minor C/C allele and absence of homozygous major allele A/A were observed only in diabetic participants; no homozygous minor C/C allele were found in normoglycemic participants. In DPP4, homozygous minor G/G allele was observed in all diabetic participants; most normoglycemic participants were observed with homozygous minor G/G allele and the remaining with heterozygous A/G allele. Genotyping of TCF7L2, however, did not provide substantial results. Conclusion: Incidence of minor alleles for the SNPs were found to be higher in the diabetic participants relative to the normoglycemic participants. Results can be potentially used for association studies and develop a prognostic tool for T2DM in Filipinos.