A sensitive and selective liquid chromatographic-tandem mass spectrometric (LC-MS/MS) method was developed and validated for the trace analysis (> 1 ng/mL level) of 2-methyl-5-aminophenyl)-4-(3-pyridyl)-2-pyrimidine (Imp-A) a genotoxic impurity in imatinib mesylate drug substances. LC-MS/MS analysis of Imp-A was done on Inertsil C18 (150 mm × 4.6 mm) 5 μm column and 0.1% formic acid in 1000 mL of water was used as buffer in mobile phase A and acetonitrile in mobile phase B. Gradient program was developed for rapid analysis. The flow rate was 1.0 mL/min and elution was monitored by mass spectrophotometer. The method was validated as per International Conference on Harmonization (ICH) guidelines. LC-MS/MS is able to quantitate up to 1 ng/mL of Imp-A.