The combined effects of the organic modifiers and the ionic strength in the eluent on the separation of sialic acids were investigated on an anion-exchange Mono Q HR5/5 column. A log-log plot of capacity factors of sialic acids vs. eluent anion concentration demonstrates good linearity. The major retention mechanism is explained as anion exchange. Moreover, the plot of capacity factors of sialic acids vs. reciprocal of eluent anion concentration indicates that other retention mechanisms exist in addition to anion exchange. The organic modifiers (methanol and acetonitrile) in the mobile phase have significant influence on the retention time and resolution. The eluent anion concentration and the fraction of organic modifier produce a very flexible system that can be optimized for the separation of sialic acids. Five standard sialic acid derivatives have been separated by choosing a suitable eluent anion concentration and the fraction of organic modifier. The optimized conditions have been applied to separate sialic acids released from bovine submandibular mucin. 5,9-Diacetylneuraminic acid (Neu5,9Ac 2) can be separated from N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc) but is overlapped with other peaks. Neu5Ac and Neu5Gc are completely separated.