Multi-walled nanotube (MWNT) functionalisation was investigated by surface-enhanced Raman spectroscopy (SERS). The MWNTs were deposited as dilute dispersions on SERS-active substrates. We used nano-structured gold surfaces with various morphologies for our measurements. The surface enhancement effect was used to amplify the Raman signal from functional molecules bound to the nanotube walls. The recorded spectral features allowed for discrimination between the differently functionalised MWNTs. Although the present study is limited to a few examples, our measurements indicate the higher specificity obtained by the SERS approach and its possible use for a systematic study of functionalisation effects on MWNT structures.