A method is described for the separation and quantitation of unhydrolyzed carrageenan polysaccharides (molecular mass approx. 3·105 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 (3·104 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.