Exploiting the advantages of miniaturization of analytical devices we worked out conditions for the analysis of viruses, subviral particles, and virus-receptor complexes on microfluidic chips. To allow for detection via laser-induced fluorescence, the viral capsids were labelled with the fluorescent dye Cy5. We analyzed human rhinovirus serotype 2 and subviral particles, followed the complexation of the virus with a synthetic fragment of the VLDL-receptor, and tracked the heat-induced conversion of intact virions into empty capsids. In contrast to fused silica capillaries, the glass micro-channels allowed for electrophoresis of the analytes without detergent, and analyses were accomplished within few tens of seconds. This opens the avenue towards the analytics of membrane-enveloped viruses and other biological assemblies that are not stable in the presence of detergent. The chip format has the additional advantage of containment and easy disposal, making it particularly attractive for the analysis of infectious material.