One of the most promising separation techniques that have emerged during the last decade is based on the use of molecularly imprinted polymers (MIPs). MIPs are stable polymers that possess specific cavities designed for a template molecule, endowed with excellent selectivity compared to regular solid phase extraction techniques. Molecularly imprinted solid-phase extraction (MISPE) has already shown a high efficiency for the sample preparation from complex matrices. Natural products received huge attention in recent years. Indeed, the application of MISPE for the screening of natural products appears extremely interesting not only for the selective extraction of a target compound but also for the concomitant discovery of new drug candidates, promising sources of therapeutic benefits. In the present review, examples of recognition and separation of active components from natural extracts are emphasized. MIPs are very promising materials to mimic the recognition characteristics exhibited by enzymes or receptors although further developments are necessary to fully exploit their wide potential.