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Molecular imprinting is a method for creating specific cavities in synthetic polymer matrices with memory for the template molecules. To date molecularly imprinted polymers (MIPs) have obtained a strong position in materials science and technology, expanding significantly the list of functional materials. This article provides a short review of the molecular imprinting technique with special attention paid to electrosynthesized electrically conducting polymers (ECPs), polypyrrole and polyethylenedioxythiophene, as matrix materials for molecular imprinting. We describe two different ECP-based MIP systems: enantioselective thin films of overoxidized polypyrrole imprinted with L-aspartic acid and surface imprinted polyethylenedioxythiophene for selective protein adsorption.