An ultrasensitive method, capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection, has been established for analysis of oligoguluronates. The oligoguluronates were derivatized with 9-aminopyrene-1,4,6-trisulfonic acid (APTS) by reductive amination at 60°C for 3.5 h. The effect on the separation of buffer pH and buffer concentration were examined. The APTS-oligoguluronates were successfully separated within 20 min by use of acidic (pH 2.5) phosphate buffer as electrolyte and a potential of 20 kV. The method was used to monitor the oligoguluronates produced by acidic hydrolysis of homopolymeric blocks of guluronic acids.