Raltegravir is a human immunodeficiency virus (HIV) integrase inhibitor, a novel anti-AIDS drug. To quantify genotoxic impurities (GTIs), conventional analysis techniques are inadequate as a result, there is a high need to develop critical analytical methods for drug analysis using the hyphenated analytical technique. A highly sensitive and selective method was developed and validated for the estimation of genotoxic impurity in Raltegravir Active pharmaceutical ingredient (API) by using UPLC-MS/MS. The UPLC-MS/MS analysis for the quantification of GTI was performed on the symmetry C18 (150 mm×4.6 mm,3.5μm) analysis column and separation of genotoxic impurity was achieved under a gradient mode system using a mobile phase comprising 1% acetic acid as mobile phase (A) and acetonitrile as mobile phase (B) with a column temperature of 40°C and flow rate of 0.5 mL/min. A triple mass quadrupole detector was used to measure GTI by combining with the negative-electrospray ionization used in multi-response monitoring mode (MRM). The newly developed method was validated as per ICH guidelines and was able to measure GTI at 2.0 ppm for about 10mg/mL solution of Raltegravir. The %RSD obtained for GTI for six preparations was 1.74 in method precision and 2.56 during the variation of analyst, system and column on a different day. The overall %RSD of 2.73 showed the ruggedness of the method. The GTI is linear from 0.039 to 2.9ppm (LOQ to 150%) and R= 0.9998 showed good linearity. The % recovery obtained for genotoxic impurity was in the range 103.0-109.6% with %RSD 1.51-3.19 from 0.42 to 2.5ppm. The %RSD in precision and accuracy at LOQ is 1.63 and 3.19 indicating the sensitivity of the method. The newly proposed and developed high-sensitive method can be used to detect GTI in Raltegravir API and formulation.