Inverse opal monolithic flow-through structures of polyaniline (PANI) were achieved in microfluidic channels for lab-on-a-chip (LOC) applications. In order to achieve the uniformly porous monolith, polystyrene (PS) colloidal crystal (CC) templates were fabricated in channel. An inverse opal PANI structure was achieved on-chip, through a two-step process involving the electrochemical growth of PANI and subsequent removal of the template. The effect of electropolymerisation on these structures is discussed. It was found that growth time is critical in achieving an ordered structure with well-defined flow-through pores. This is significant in order to fabricate optimal porous PANI structures that maximise surface area of the monolith and also provide well-defined flow profiles through the micro-channel.