The stepwise assembly of pre-replicative complexes (pre-RCs) is essential for the initiation of DNA replication. Cdt1, a component of the pre-RC, is required for the loading of the minichromosome maintenance (MCM) complex onto chromatin. Cdt1 physically interacts with the MCM complex, and this interaction mainly occurs between Cdt1 and Mcm6 in human cells. Here we show by yeast two-hybrid analysis, co-immunoprecipitation and GST pull-down assays that the extreme C-terminal region of hMcm6 (a.a. 708-821) interacts with a short C-terminal region in hCdt1 (a.a. 392-471), while the large N-terminal part of hMcm6 (a.a. 1-707) interacts with some other MCM subunits. Furthermore, our functional studies show that ectopic expression of either of the interacting domains of hCdt1 and hMcm6 in human cells reduces chromatin association of the MCM complex and DNA replication, inhibits cell proliferation, and leads to cell apoptosis. These dominant negative effects indicate that the interaction between hCdt1 and hMcm6 through their interacting domains we identified is the key for hCdt1 in facilitating the MCM hetero-hexamer to load onto chromatin for replication licensing. The newly indentified interacting domains of hCdt1 and hMcm6 may become targets for identification of novel anticancer drugs.