A method is described for the separation and quantitation of unhydrolyzed carrageenan polysaccharides (molecular mass approx. 3·10 5 rel. mol mass) by capillary electrophoresis. Various carrageenan samples were first derivatized with the fluorescent reagent, trisodium 8-aminopyrene-1,3,6-trisulfonate (APTS), in both laboratory and commercial blend samples. Microcentrifuge filters (3·10 4 rel. mol. mass) were then employed to separate derivatized samples into low (eluate) and high (retentate) molecular mass fractions which could each be assayed by CE with laser-induced fluorescence detection. Eluate fractions contained small amounts of kappa and iota species which could be efficiently separated by capillary zone electrophoresis (CZE) using a buffer with an anti-convective additive. Separation of species contained in the retentate fraction (kappa, iota, lambda) could be achieved in under 5 min by CZE using a citrate buffer, pH 3.0. The influence of the pre-filtration step, field strength and temperature on peak efficiency and resolution are studied. Quantitative aspects are evaluated and the method then applied to real commercial samples of food additive mixtures.