In 1995, the Nucleic Acids Research Group (NARG) of the Association of Biomolecular Resource Facilities (ABRF) eval-uated the quality of common oligonucleotides synthesized at core facilities and determined that these facilities provided products of high quality. In a 1999 survey, it was determined that most academic DNA synthesis core facilities regularly provide "boutique oligos," or modified oligonucleotides; how-ever, the quality of these products has not been the focus of a specific study. The NARG therefore designed an internal study whereby a standard oligonucleotide (M13F) and mod-ified forms of the oligonucleotide, including: 5Biotin, 5 TET (tetrachlorinated 6-carboxyfluorescein), and an antisense oligonucleotide using phosphorothioate chemistry, were syn-thesized by NARG members' laboratories. The products were then analyzed by matrix-assisted laser desorption ion-ization–time of flight mass spectrometry (MALDI-TOF MS), electrospray ionization mass spectrometry (ESI-MS), capillary electrophoresis (CE), and urea-gel electrophoresis.The qual-ity of the synthesis of these oligonucleotides as assessed by these methods are reported in this work along with a dis-cussion about the utility of these various quality-assurance technologies. (J Biomol Tech 2001;12:16–24) KEY WORDS: capillary electrophoresis, gel electrophoresis, mass spectrometry, modified oligonucleotides, oligonu-cleotides, quality assurance.