For the first time, a capillary electrophoresis-time of flight-mass spectrometry analysis method for detecting anthocyanins in red onion was developed. The analysis method included the use of silica capillaries coated with poly-LA 313 (polycationic amine-containing polymer) and an MS-compatible volatile background electrolyte (BGE). The method was environmentally friendly and sensitive; and its rapidness combined with an acidic BGE helped in preventing anthocyanin degradation. By using high-resolution TOF-MS with pre-run tuning of masses, low mass errors were achieved in the determination of conjugated anthocyanins in red onion, and a simultaneous up-front fragmentation provided confirmation of the aglycon backbone for their secure identification. Most anthocyanins (at least seven out of ten) known in red onion from the literature were found, as well as one new for this matrix.