Halloysite is aluminosilicate clay with hollow tubular structure. Biocompatibility study is important for its potential application in controlled drug delivery. Halloysite nanotubes were added to different cell cultures for toxicity tests. Its fluorescence functionalisation by APTES and with fluorescently-labeled polyelectrolyte layers allowed following halloysite uptake by the cells with Confocal Laser Scanning Microscopy (CLSM). Quantitative Trypan blue and MTT measurements performed with two neoplastic cell lines model systems as function of the nanotubes concentration and incubation time indicate that halloysite exhibits a high level of biocompatibility and very low cytotoxicity, rendering it a good candidate for household materials and medicine. A combination of Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM) and Scanning Force microscopy (SFM) imaging techniques have been employed to elucidate the structure of halloysite nanotubes.