Protein-polysaccharide conjugate vaccines offer the prospect of reducing morbidity and mortality due to bacterial pneumonia and meningitis but, because of their size and heterogeneity, are often a challenge to characterize by traditional analytical methods. Vaccines consisting of Streptococcus pneumoniae, or Neisseria meningiditis polysaccharide covalently linked to formaldehyde-inactivated diphtheria toxoid carrier protein were resolved from non-conjugated toxoid by micellar electrokinetic chromatography. Separation was achieved using alkaline sodium borate solutions containing sodium dodecyl sulfate in excess of the critical micellar concentration. No sample pretreatment was required prior to analysis. Diphtheria toxoid peak migration times were highly reproducible. Measurement of absolute toxoid peak area showed poor precision, but good precision was observed when peak area was normalized against an internal standard (myoglobin). Good linearity was observed over useful ranges of both protein content and injection time.