The aim of the present study was to develop an analytical method for measuring amounts of a dendrofullerene (DF) which is a highly water-soluble fullerene derivative. We tried to define a straightforward methodology using capillary zone electrophoresis, a method which, to our knowledge, has not yet been used to that purpose. Preliminary assays showed that DF has almost the same mobility than the electroosmotic flow (EOF) but in the opposite direction. Attempts were carried out to reduce the EOF and positive results were obtained by adding hydroxypropylcellulose to the background electrolyte. In order to define optimal operating conditions, a Taguchi experimental plan was used to study simultaneously the effects of the main parameters that are pH, ionic strength, methanol amount and hydroxypropylcellulose concentration. Two parameters are of the utmost importance as to their effect on the migration time and separation efficiecy: pH and ionic strength whose actions are opposite.