Background. Homoeopathic medicines treat diseases, including cancer, using ultradiluted preparations. Earlier studies indicated that homoeopathic medicines are cytotoxic to tumor cells and reduced animal tumors. However, the mechanism of homoeopathic medicines at the cellular level is not known.Methods. The following drugs were used in the study: Ruta 200C, Carcinosinum 200C, Hydrastis 200C, Thuja 200C, and Thuja 1M. These drugs were tested for their ability to induce apoptosis as seen by morphology, DNA laddering, expression of genes related to apoptosis, and TUNEL assay. Similarly, the effect of homoeopathic medicines on apoptosis was measured by microarray analysis. Activity of Ruta 200C was compared with that of the mother tincture.Results. Ruta 200C produced morphological changes in the Dalton’s lymphoma ascites tumor cells and induced DNA laddering. Carcinosinum 200C increased apoptotic gene p53 and Ruta 200C decreased antiapoptotic gene Bcl2. Administration of potentiated homoeopathic drugs to tumor-bearing mice induced TUNEL-positive cells in the tumor, showing increased apoptosis of tumor cells. Microarray analysis of cells treated with homoeopathic drugs indicated that many enzymes related to apoptosis were increased by homoeopathic drugs.Conclusion. These data indicate that apoptosis is one of the mechanisms of tumor reduction of homeopathic drugs. A comparison of potentiated drugs with their mother tincture indicated that the potentiated drugs have biological activity similar to that of their mother tincture in spite of ultradilution.