Capillary electrophoresis (CE) has been applied to the study of complexation between dextrins and polyiodides. A baseline separation of fluorescently labeled dextrin oligomers has provided a unique platform for the observation of a contribution of single oligomers to the complexation process that could previously be measured only in bulk. The complex formation was easily recognized through comparison of peak migration times and peak shapes in the presence and absence of polyiodides. The degree of polymerization (DP) number was found crucial in the binding process, but the I-2/I- ratio in a solution also appeared to determine the nature of complexation. The effects of buffer pH and ionic strength upon complexation were also briefly investigated. Diode-array spectra in the visible wavelength range confirmed the differential complexation of unlabeled maltodextrins with different DP values after a CE iodine affinity separation. C-13-nuclear magnetic resonance (NMR) spectral data on differently sized dextrin fractions were found to be in good agreement with the results from CE measurements.