Carbon nanomaterials possess unique structural and physicochemical properties, and thus they are broadly utilized as carriers for a variety of therapeutic agents in nanomedicinal applications. Herein we present an electrochemical characterization of binding capability of acidic oxidized multi-walled carbon nanotubes (oMWCNTs) modified with poly(ethylene glycol) towards common cytostatic drug etoposide (or VP-16). The comparison of willingness of oMWCNTs and MWCNTs-PEG to form complexes with etoposide revealed significantly higher capacity in PEGylated variant of carbon nanotubes (the 15 mM etoposide loading capacity was approximately 46.4% in 2 mg of MWCNT-PEG or 28.1% in equal amount of oMWCNT). To obtain a multifunctional nanotransporter we employed the phosphorothioate oligodeoxynucleotide (PODN), which could further extend the possible biological effects of MWCNT-PEG-Etoposide complex. By using square wave voltammetry, the binding capacity of 2 mg of MWCNT-PEG-Etoposide (15 mM) towards PODNs was determined to be 4.5 µM. Such characterized multifunctional complex can be further employed for biological testing on chemoresistant tumors, such as non-small-cell lung cancer, to enhance the treatment efficiency.