Baseline separation of seven paralytic shellfish toxins (PSTs), namely decarbamoylsaxitoxin (dcSTX), saxitoxin (STX), neosaxitoxin (NEO), gonyautoxin-2 (GTX-2), gonyautoxin-3 (GTX-3), gonyautoxin-1 (GTX-1), and gonyautoxin-4 (GTX-4), was achieved by using capillary ITP (CITP)/CE with UV detection. Separation parameters including duration time and voltage in CITP process, separation voltage, and pH and concentration of buffer were optimized. The developed method provided linear responses from 1.3 to 200 microM for the PSTs. The LOD ranged from 0.1 to 0.3 microM. PST extracts from two algal strains of Alexandrium tamarense were analyzed and the toxin concentrations in the samples were quantified with an internal standard method by using NEO as the internal standard. The algal extract of A. tamarense HK9301 contained 332 microM GTX-2 and 224 microM GTX-3, while the PSTs were not detected in the extract of A. tamarense CI01.