We have studied the energy loss of protons in multi-walled carbon nanotube (MWCNT) samples, both experimentally and theoretically. The experiments were done in transmission geometry, using 6 and 10 keV proton beams, with the MWCNT targets dispersed on top of a similar to 20 nm-thick holey carbon coated TEM grid (amorphous carbon film, a-C). The energy loss of protons interacting with the MWCNTs and the amorphous carbon film is obtained after analyzing the signals coming from both types of carbon allotropes. The electronic energy loss of protons is calculated using the dielectric formalism, with the target energy loss function built from optical data. Comparison of experimental and theoretical data indicates that model calculations appropriate for three-dimensional (bulk) targets substantially overestimate the energy loss to MWCNTs. In contrast, a recent parameterization of the dielectric function of MWCNTs predicts significantly lower stopping power values compared to the bulk models, which is more in line with the present experimental data when considering the additional stopping mechanisms that are effective in the key range. (C) 2010 Elsevier B.V. All rights reserved.