Although the major activities of traditional remedies have mostly been known since ancient times, their molecular mechanisms of action have usually not been investigated in much detail. The pharmaceutically relevant activities of botanical therapeutics frequently result from additive or synergistic effects of a multitude of components. Several studies have been published that analyze the effects of complex preparations on selected in vitro model cell systems by using gene expression analysis. Herein, the examples referred to include transcriptional studies with extracts from Ginkgo biloba and Echinacea as well as the Tibetan Formula Padma 28. Transcriptional profiles can be used to deduce key molecules and pathways affected upon treatment. Differentially expressed gene sets can further be integrated with information derived from interaction databases, thus giving a more comprehensive view of activated biological processes. Transcriptomics, by using microarray technology, is used as a tool in different fields of natural product research, ranging from activity monitoring to toxicity profiling.