Two series of genistein (=5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-1-benzopyran-4-one) derivatives with heterocycles were prepared, in which genistein and heterocyclic moieties were separated by C(2) and C(3) spacers. Among the 24 compounds we prepared, 22, i.e., 3a-3k and 4a-4k, were reported for the first time, while the preparation of 2a and 2b was reported in our recent paper. The cytotoxic activities of these compounds were evaluated against human chronic myeloid leukemia cells (K562) and a human nasopharyngeal epidermoid tumor cell line (KB). Compounds 4a, 4d, 4e, 4h, and 4i showed remarkable anticancer activities in vitro that are comparable with 5-fluorouracil, an canonical anticancer drug. Structure-effect relationships were also discussed based on the experimental data obtained.