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3-D integration technology is emerging as an attractive alternative to increase the transistor count for future chips. The majority of the existing 3-D integrated circuit (IC) research is focused on the performance, power, density, and heterogeneous integration benefits offered by 3-D integration. All such advantages, however, ultimately have to translate into cost evaluation when a design strategy has to be decided. Consequently, system-level cost analysis at early design stages is imperative to decide on whether 3-D integration should be adopted. This paper presents a cost estimation method for 3-D ICs at early design stages and proposes a set of cost models that include wafer cost, 3-D bonding cost, package cost, and cooling cost. The proposed 3-D IC cost estimation method can help designers analyze the cost implication for 3-D ICs during the design space exploration at the early stage, and it enables a cost-driven 3-D IC design flow that can guide the design choice toward a cost-effective direction. Based on the proposed cost estimation method, this paper demonstrates two case studies that explore the cost benefits of 3-D integration for application-specific integrated circuit designs and many-core microprocessor designs style, respectively. Finally, this paper suggests the optimum partitioning strategy for future 3-D IC designs.