Molecular mechanics and molecular dynamics simulations have been employed to characterise the interactions between SWNTs and biocompatible amphililic derivatives of chitosan, namely N-butyl-O-sulfate chitosan (NBSC), N-octyl-O-sulfate chitosan (NOSC) and N-palmitoyl-O-sulfate chitosan (NPSC). The computational simulations have shown that the affinity of the polymer for the hydrophobic surface of the nanotubes depends on the length of the chitosan hydrophobic pendant chain. Longer chains have a higher flexibility and therefore a better ability to wrap around the nanotubes. To underpin the theoretical calculations, experimental studies revealed that NPSC exhibits highest affinity for SWNTs with up to 66.9 ± 19.7% SWNTs stably suspended in an aqueous environment; this affinity was confirmed by the calculated binding energy of five polymer chains with a SWNT that was found to be -300.93 kcal mol(-1), the highest amongst the three polymers studied. Furthermore, the high value of cell viability after incubation with NPSC indicates that this is a good candidate for the preparation of biocompatible SWNTs dipersions that could be used in biomedical and pharmaceutical applications.