Nuclear magnetic resonance (NMR) spectroscopy has been used for structural characterization of 5-fluorouracil (5FU) & daunorubicin (DAU) co-loaded poly(butylcyanoacrylate) nanoparticles (PBCN), prepared by an anionic polymerization of n-butylcyanoacrylate, probing two different drug loading approaches. Diffusion ordered spectroscopy, obtained through pulsed field gradient NMR experiments, has been performed to determine the overall structure of the 5FU & DAU co-loaded PBCN and to clarify the mechanisms of drug immobilization and location in the polymer matrix of PBCN. Physicochemical properties such as composition, size, surface chemistry and shape have been defined. All data obtained have been referred to the dual drug-loading procedures employed. The results show that 5FU & DAU co-loaded PBCN can be designed to exhibit different properties, composition and overall structure, depending on the method of preparation. The structural attributes relate to the drug efficacy and reactivity characteristics such as capacity for sustained drug release, targeted drug delivery, drug penetration, retention in and transport through bio-membranes. The design of nanoparticle platforms to deliver multiple drugs for combination therapy offers the opportunity for novel strategies in an effort to increase the efficacy of cancer therapy.