Ion-pair reversed-phase non-denaturing IP-RP LC method is suitable for separation of single stranded impurities from siRNA duplex. The optimized ion pairing system permitted separation and characterization of two siRNA duplexes present in the drug formulation. Mobile phase was compatible with MS detection which permitted the confirmation of eluting species according to their molecular weight. We demonstrate that ACQUITY Premier Peptide BEH C18, 300 Å Column is suitable for robust quantitation of siRNA duplexes without compromises or carryover. The ACQUITY Premier Column afforded higher confidence in accuracy of quantitation; its performance fulfils the quality requirements for the qualification parameters of recovery, repeatability, and linearity.