The field of carbon nanotube-amphiphile self assembly has been reviewed to address the ongoing debate regarding their binding. Based on our spectrophotometry and transmission electron microscopy studies, this report shows the binding of lysophospholipids onto carbon nanotubes is dependent on the charge and geometry of the lipids and the pH of the solvent, and independent of solvent temperature. From molecular dynamics simulations, the binding of lysophospholipids onto carbon nanotubes does not fully obey any of the models proposed in the literature. We also studied carbon nanotube diffusion using single-molecule fluorescence microscopy, and carbon nanotube-lipid binding and dissociation using the technique of fluorescence resonance energy transfer. The use of carbon nanotube-lipid assembly for enabling nanotoxicological studies is demonstrated by the uptake of the assembly in the living organism Daphnia magna.