Rutin, a strong antioxidant, has been implicated in the prevention of liver inflammation. However, low solubility and permeability through the gut wall limit development of rutin as a therapeutic agent for oral administration. Phytosomes are described as lipid nanocarriers with a complexation between the phospholipid headgroups and entrapped phytochemicals. The aim of this research was to compare the structure of rutin liposomes to rutin phytosomes. FT-IR, DSC and NMR were employed to investigate the presence of any molecular interactions between the formulation components. The FT-IR spectra showed that a new –OH bond had formed in the rutin phytosomes, suggesting the formation of a molecular complex. 31P NMR experiments revealed that the DPPC molecule is altered when formulated as liposomes but that these changes were greater for samples from the phytosome formulation. DSC data revealed that when rutin was added to DPPC there was a significant shift in the transition temperature of DPPC. Further, the shift was greater in the THF solvent used to produce phytosomes compared to CHCl3 used to produce liposomes. 1H NMR spectra of the phytosome samples indicated three additional peaks that were greater than in the liposome formulation. ROESY NMR spectra provided evidence supporting the interaction between rutin and DPPC in both liposomes and phytosomes. The apparent differences in molecular interaction between liposomes and phytosomes did not however impact rutin release in biorelevant media or during in vitro small intestinal lipolysis.