Bioanalysis of oligonucleotides by HPLC-MS/MS in support of regulatory submission has not been widely adopted. Several obstacles such as lack of sensitivity, adduct formation and analytical instrument dedication are barriers that many laboratories are unwilling to challenge. In order to increase the sensitivity of the method, analysis was conducted using microflow HPLC (MFLC) conditioned for oligonucleotide analysis thus reducing adduct formation. The microflow system is on a portable cart that allows the scientist the ability to transport the pumps to any mass spectrometer available without allocating an entire LC-MS/MS system for oligonucleotide analysis. HPLC-MS/MS analysis is an alternative approach to ELISA and qPCR analysis providing better selectivity, increased dynamic range and the flexibility to analyze a vast array of oligonucleotides from any biological matrix.