It is established that amphiphilic beta-cyclodextrins chemically modified with alkyl chains on the secondary face exhibit self-organisation properties yielding stable nanospheres or nanoparticles. The ability of these promising colloidal drug carriers to encapsulate drugs being partly related to the internal structure of nanosystems, precise characterisation methods are required to control their synthesis procedure. The present work describes the development of complementary analytical methods based on reversed-phase high-performance liquid chromatography (RPLC) coupled to evaporative light-scattering detection (ELSD) and electrospray ionisation-mass spectrometry (ESI-MS) to characterize various beta-cyclodextrins enzymatically transesterified by vinyl-acyl fatty esters (the number of carbon atom in the acyl chain varying from 4 to 12). LC-ELSD has been used in a preliminary step to optimize the separation on a monolithic octadecylsiloxane-bonded silica stationary phase. A complex fingerprint was achieved for each mixture, revealing the presence of isomers unnoticed by the sole spectrometric (NMR and MS) techniques.