Herbal extracts with antioxidant properties are enjoying increasing popularity as remedies for acute and chronic illnesses such as depression, memory loss, cardiovascular disorders and immunological deficiencies. The molecular targets of these complex mixtures of botanical extracts are poorly understood. We have evaluated a well-characterised herbal extract for its ability to affect the mRNA expression profile of a human cancer cell line. We used the Affymetrix hu6800 set of DNA microarrays chip to define changes in the mRNA expression profile of cells exposed to the herbal extract for 6 hours, 48 hours and 72 hours. The target RNA extracts hybridised to 32.3% of the probes on the chip. Of the 2,200 transcripts, 400 transcripts were altered by the extract over time. Two transcripts for antioxidant enzymes were up-regulated (>threefold at 6 hours). Eighteen transcripts with a high basal expression were down-regulated and this group is associated with invasive growth. Sixteen transcripts expressed at low levels behaved as in the previous group and included transcripts for members of the MAP kinase family and signal transducing proteins. Eighteen transcripts were up-regulated and peaked at 48 hours followed by return to basal levels; this group consisted of transcription factors. The largest group of 274 transcripts was up-regulated approximately twofold through the course of the exposure to the extract and included a broad group of transcripts. Our data demonstrate that the Affymetrix hu6800 microarrays can be used to define the molecular targets of a complex mixture of a botanical extract on human cells in culture. This strategy can also be used for a more rational evaluation of the biological activities of sub-fractions and the individual components of such a complex herbal extract.