Polyaniline (PAni) is an example of a conducting polymer that can be switched between an insulating and a conductive state. This switching is accompanied by a colour change. Recently, interest has developed in the nanofibre form of PAni as these low dimensional structures have a very high surface area, thus enabling a faster response time. We investigate how the surface chemistry of these nanofibres can be modified by covalently attaching functional side-groups. In particular, we demonstrate the attachment of both amide and carboxylic acid groups. This can be achieved using a simple reflux technique. The modified material retains its nanomorphology and the intrinsic electrochemical, spectroscopic and redox properties of PAni are also preserved. Both acid and amine side-groups are interesting in that they provide a template, which could be further altered to enhance the selectivity of PAni. Acid terminated chains can also be used to introduce self-doping behaviour to PAni.