Aim: Carbon nanotubes (CNTs) are increasingly being utilized in neurological applications as components of implants, electrodes or as delivery vehicles. Any application that involves implantation or injection of CNTs into the CNS needs to address the distribution and fate of the material following interaction and residence within the neuronal tissue. Here we report a preliminary study investigating the fate and structural integrity of amino-functionalized CNTs following stereotactic administration in the brain cortex. Materials & methods: The CNTs investigated had previously shown the capacity to internalize in various cell types of the CNS. An aqueous suspension of multiwalled CNT-NH3 + was stereotactically injected into the mouse brain cortex. Their interaction with neural cells and consequent effects on the CNT structural integrity was investigated by optical, transmission electron microscopy and Raman spectroscopy of brain tissue sections for a period between 2 and 14 days post cortical administration. Results & discussion: The occurrence of severe nanotube structure deformation leading to partial degradation of the chemically functionalized-multiwalled CNT-NH 3 + in vivo following internalization within microglia was revealed even at early time points. Such initial observations of CNT degradation within the brain tissue render further systematic investigations using high-resolution tools imperative. © 2012 Future Medicine Ltd.