The synthesis and cytotoxic evaluation of a series of Fmoc-based dipeptides are described. Among the thirty compounds, 4a, 8a, 12a, 2b, 4b, 10b, 3c, 4c and 6c showed potent activity against HepG2, Hep3B, MCF-7, MDA-MB-231, A549 and Ca9-22 human cancer cell lines. The most active compounds (10a and 10c) showed relatively good sensitivity toward HepG2 and Ca9-22 cell lines with IC50 values of 1.0 and 0.4 microM, respectively. Additionally, compound 10c was threefold more potent than doxorubicin, the positive control, against the Ca9-22 cell line. Furthermore, 10c showed a synergistic effect and increased the cytotoxicity of doxorubicin against the MDA-MB-231 cancer cell line. Therefore, 10c could be used as a new lead compound for therapeutic development.