Nanostructured films from two conducting polymers, poly(o-methoxyaniline) (POMA) and poly(3-thiopheneacetic acid) (PTAA), were fabricated with the layer-by-layer (LBL) technique. The electrochemical response of the LBL films differs from that of a POMA cast film, even in a potential range where PTAA is inactive. This is attributed to differences in the diffusion-controlled charge and mass transport, where distinct ionic species participate in the LBL films, as demonstrated by quartz crystal microbalance measurements. The results show that the transport properties of conducting polymers can be changed by alternation with layers of appropriate materials in LBL films.