Inverse opal monolithic flow-through structures of conducting polymer (CP) 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 microfluidic channels. Consequently, an inverse opal polyaniline (PANI) structure was achieved on-chip, through a two-step process involving the electrochemical growth of PANI and subsequent removal of the template. In this work the effect of CP electropolymerisation time 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 as these optimised porous structures will allow for maximising the surface area of the monolith and will also result in well-defined flow profiles through the microchannel.