Surface modification of natural halloysite clay nanotubes with γ-aminopropyltriethoxysilane (APTES) was investigated. Untreated and modified samples were characterized by nitrogen adsorption, X-ray diffraction, elemental analysis, thermogravimetry, transmission electron microscopy, atomic force microscopy, MAS nuclear magnetic resonance (²⁹Si, ¹³C, ²⁹Al), and Fourier transform infrared spectroscopy. The modification mechanism was found to include not only the direct grafting of APTES onto the hydroxyl groups of the internal walls, edges and external surfaces of the nanotubes but other processes in which oligomerized APTES condensed with the directly grafted APTES to form a cross-linked structure. The thermal and evacuation pretreatment conditions were found to play an important role in controlling the extent and mechanism of the modification. The extent of modification is also strongly affected by the morphological parameters of the original clay samples. This study demonstrates that the surface chemistry of halloysite nanotubes is readily modified, enabling applications in nanocomposites, enzyme immobilization and controlled release.