The development and implementation, at the end of the '50s, of two poliovirus vaccines was responsible for a huge drop of poliomyelitis patients worldwide. In 1988, the Global Polio Eradication Initiative was launched to eliminate the virus by 2000. During these, ongoing, last steps to reach eradication and in the post-eradication era, the combination of a fast diagnosis of polio patients and environmental contamination and effficient treatment with antipolioviral therapy of the infected patients will be of critical importance. At this moment however, neither a fast diagnostic device nor an appropriate therapy is available to comply with the calls of the Polio Research Committee. Here, the use of capillary electrophoresis was investigated as an alternative technique to identify poliovirus and for the evaluation of the formation of nanobody-poliovirus complexes, and therefore predicting the in vitro neutralizing potential of nanobodies. The developed CE method can be used as a rapid, qualitative screening for the affinity between poliovirus and nanobodies, based on a clearly visible and measurable shift in migration time on the electropherogram.