Capillary zone electrophoresis was applied to separate caseinoglycomacropeptide glycoforms and characterize microheterogeneity of the glycopeptide. Particular attention was paid to the sialic acid content in caseinoglycomacropeptide obtained through different manufacturing processes. A chemometric approach was used to simultaneously study effects of acid concentration, hydrolysis time and temperature on sialic acid release from caseinoglycomacropeptide. Hydrolysis conditions that maximize sialic acid release were chosen. Sialic acid was determined using high performance anion exchange chromatography coupled with pulsed amperometric detection. Results were compared to those obtained by alternative techniques, such as colorimetric and enzymatic methods.