Biomedical applications of functionalised carbon nanotubes (f-CNTs) for imaging as well as drug or gene delivery in the brain have recently gained interest. Several studies have demonstrated the potential of f-CNTs to offer treatment options for neurological conditions with success. However, there is also evidence that f-CNTs accumulate preferentially within microglial cells when introduced in the brain. Considering the key immunologic role of these cells in the brain and the limited knowledge regarding the interaction of CNTs with microglial cells, it is imperative to understand whether accumulation of CNTs in microglial cells can alter their physiological functions or trigger pro-inflammatory signalling. The aim of the present study was to investigate the basic physiological functions of isolated primary microglial cells over time, following their exposure to multi-walled carbon nanotubes functionalized via different surface chemistries. We rationalized that some chemical strategies may be more deleterious for microglial cell functions than others. We used rat primary microglial cells that can be maintained in cell culture for a long period of time without undergoing cell division. Cell viability, phagocytosis, migration, pro-inflammatory factor release were studied over one month, following a single exposure to a non-cytotoxic concentration of three different f-CNTs (carboxylated, aminated and both carboxylated and aminated). We show that f-CNTs do not induce inflammation and are not affecting basic functions of microglial cells under these conditions. Importantly, this was the case from day 1 to day 28 post-exposure, even though microglial cells had internalized f-CNTs in subcellular compartments and retained the nanotube load in their cytoplasm over time.