A newly synthesized indole-derivative is able to induce cytostatic and cytotoxic effects in the colon cancer cells HT29, effecting apoptosis by activation of an intrinsic pathway. Magnesium is involved in both cell growth and apoptosis even though its role in the latter process is not well defined. The aims of this work were: firstly, to verify if magnesium content is related to the proliferative rate in HT29 cells; secondly, to assess the involvement of the cation in mitochondria-mediated apoptosis triggered by the new antiproliferative molecule. The effects of the indole-derivative in treated cells included cell-cycle arrest in the G2/M phase, and apoptotic death confirmed by release of cytochrome c from the mitochondrial compartment. Moreover, we demonstrated that the basal content of magnesium in HT29 cells inversely correlates with cell saturation density. In addition, a decrease in both free and intracellular total magnesium concentration was observed along with the induced apoptosis. Taken together, these data suggest that magnesium participates in the complex signaling network of cell proliferation and apoptosis.