LC/MS method development was undertaken to investigate the factors affecting the separation of anthocyanin-3-O-glucosides in fractionated wine samples. The type and concentration of acid used to lower the pH of the HPLC solvents was found to be the most critical factor, with formic acid producing far better separations than acetic acid. The choice of solvent gradient, column temperature and flow rate were also found to affect separation. The methods thus developed were successfully applied to the separation (by HPLC) and identification (by PDA/UV-Vis and MS) of a number of anthocyanin-3-O-glucosides, anthocyanin- 3-O-acylglycosides, pyranoanthocyanins and polymeric pigments in young Pinot Noir and Cabernet Sauvignon wines. The relative amounts and proportions of anthocyanin-3-O-glucosides were compared between young wines vinified from four varieties of grape (Cabernet Sauvignon, Malbec, Merlot and Syrah) sourced from the Marlborough region of New Zealand.