Effective methods for localization and characterization of bioactivity are a cornerstone for natural product based drug discovery efforts. Over the last decade, a wealth of new technologies and conceptual approaches for bioactivity screening have emerged. These developments are reviewed under the perspective of their applicability in the field of natural products discovery. The methods discussed here include bioautography, HPLC-based activity profiling, HPLC-based on-flow bioassays, assays based on capillary electrophoresis, molecular imprinted polymers, various MSand NMR-based methods, biosensors, and chip-based technologies for affinity separation and expression profiling. Selected examples illustrate the potential and limitations of the different approaches for contemporary natural products lead discovery.