This article concerns the effect of pristine, carboxylic and amino-functionalised carbon nanotubes used as filler in epoxy-based nanocomposites. The amount of carbon nanotubes was within the range 0.2–0.8 wt%. Their mechanical properties were investigated by means of flexural strength and resilience tests. The carbon nanotubes lead to an improvement of ductility and mechanical strength compared to the neat epoxy resin in the order: amino > carboxylic > pristine. The results of morphological, calorimetric, rheological and electrical conductivity tests suggest that this improvement is due to a good dispersion of the filler in the matrix and it occurs especially with low filler amounts (0.2–0.4 wt%) of amino carbon nanotubes. In the nanocomposites realised with amino-functionalised carbon nanotubes there is an interphase that creates a weak interfacial interaction between the filler and the epoxy resin. The thermal stability as well as the electrical conductivity of resin, is not appreciably improved after the addition of either functionalised carbon nanotubes.